Origin IGS: ggagaaattaaaagattctagggcatctctaaaaaccttgttggatttgcttcgcgtccttcggaatagagatgccctttaatttgtttctttttgcgaatac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtattcgcaaaaagaaacaaattaaagggcatctctattccgaaggacgcgaagcaaatccaacaaggtttttagagatgccctagaatcttttaatttctcc Mask Tandem Repeat Region ================================================ ggagaaattaaaagattctagggcatctctaaaaaccttgttggatttgcttcgcgtccttcggaatagagatgccctttaatttgtttctttttgcgaatac Find is-nt database================================================ Query_seq: TDE1090:TDE1091|TDE1090:TDE1091:threonyl-tRNA synthetase:hypothetical protein:-><-:1123004..1123106 103 ggagaaattaaaagattctagggcatctctaaaaaccttgttggatttgcttcgcgtccttcggaatagagatgccctttaatttgtttctttttgcgaatac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1090:TDE1091|TDE1090:TDE1091:threonyl-tRNA synthetase:hypothetical protein:-><-:1123004..1123106 103 ggagaaattaaaagattctagggcatctctaaaaaccttgttggatttgcttcgcgtccttcggaatagagatgccctttaatttgtttctttttgcgaatac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1090:TDE1091|TDE1090:TDE1091:threonyl-tRNA synthetase:hypothetical protein:-><-:1123004..1123106 103 ggagaaattaaaagattctagggcatctctaaaaaccttgttggatttgcttcgcgtccttcggaatagagatgccctttaatttgtttctttttgcgaatac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggagaaattaaaagattctagggcatctctaaaaaccttgttggatttgcttcgcgtccttcggaatagagatgccctttaatttgtttctttttgcgaatac Predict ORF larger than 30AA ================================================ ggagaaattaaaagattctagggcatctctaaaaaccttgttggatttgcttcgcgtccttcggaatagagatgccctttaatttgtttctttttgcgaatac 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================================================ ggagaaattaaaagattctagggcatctctaaaaaccttgttggatttgcttcgcgtccttcggaatagagatgccctttaatttgtttctttttgcgaatac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1090:TDE1091|TDE1090:TDE1091:threonyl-tRNA synthetase:hypothetical protein:-><-:1123004..1123106 103 ggagaaattaaaagattctagggcatctctaaaaaccttgttggatttgcttcgcgtccttcggaatagagatgccctttaatttgtttctttttgcgaatac Intra-Species Hit: Count: 1 Min: 1 Max: 103 Len: 103 Subject: NC_002967_TDE1090_TDE1091|threonyl-tRNA synthetase:hypothetical protein|POSITIVE:NEGATIVE|[1123004,1123106]|103 HSP 1 e-value: 4.0E-52 bit: 204.0 Len: 103 Query Start:1 Query End:103 Subject Strand: POSITIVE Subject Start: 1 Subject End: 103 ggagaaattaaaagattctagggcatctctaaaaaccttgttggatttgcttcgcgtccttcggaatagagatgccctttaatttgtttctttttgcgaatac ggagaaattaaaagattctagggcatctctaaaaaccttgttggatttgcttcgcgtccttcggaatagagatgccctttaatttgtttctttttgcgaatac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAGAAAUUAAAAGAUUCUAGGGCAUCUCUAAAAACCUUGUUGGAUUUGCUUCGCGUCCUUCGGAAUAGAGAUGCCCUUUAAUUUGUUUCUUUUUGCGAAUAC ((((((((....(((((..((((((((((((....((.....((((..((...))))))...))..))))))))))))..))))))))))))).......... (-30.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAUUCGCAAAAAGAAACAAAUUAAAGGGCAUCUCUAUUCCGAAGGACGCGAAGCAAAUCCAACAAGGUUUUUAGAGAUGCCCUAGAAUCUUUUAAUUUCUCC .........((((((......((..((((((((((((..((...(((.((...))...))).....))....))))))))))))..))))))))......... (-25.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 63 21 226 170 NC_002967:TDE1073|5end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1103515..1103745_POSITIVE 309 76 36 210 156 NC_002967:TDE0190|5end_hypothetical_protein_227366..227596_NEGATIVE 303 100 54 66 8 NC_002967:TDE1676|5end_ribosomal_protein_S18_1729642..1729872_NEGATIVE 299 80 35 153 94 NC_002967:TDE1522|5end_citrate_lyase_ligase_1567780..1568010_POSITIVE 295 80 33 159 110 NC_002967:TDE2021|5end_hypothetical_protein_2044759..2044989_NEGATIVE 295 78 37 148 106 NC_002967:TDE0596|5end_hypothetical_protein_636010..636240_NEGATIVE 295 99 58 54 1 NC_002967:TDE0487|5end_ABC_transporter,_ATP-binding_protein_544413..544643_NEGATIVE 293 64 29 66 37 NC_002967:TDE1726|5end_polyA_polymerase_family_protein_1779546..1779776_POSITIVE 290 59 19 172 119 NC_002967:TDE1098|5end_hypothetical_protein_1133678..1133908_NEGATIVE 289 60 19 51 5 NC_002967:TDE0987|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1014041..1014271_POSITIVE 289 88 43 221 160 NC_002967:TDE0397|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_446777..447007_POSITIVE 281 69 30 227 180 NC_002967:TDE1589|5end_purine-binding_chemotaxis_protein_1637004..1637234_POSITIVE 281 98 51 222 184 NC_002967:TDE0790|5end_30S_ribosomal_protein_S11_816951..817181_POSITIVE 280 59 11 165 119 NC_002967:TDE2736|5end_hypothetical_protein_2791812..2792042_NEGATIVE 275 100 59 79 47 NC_002967:TDE2657|5end_precorrin-2_C20-methyltransferase,_putative_2693822..2694052_POSITIVE 275 75 38 116 83 NC_002967:TDE1652|5end_ABC_transporter,_ATP-binding/permease_protein_1700524..1700754_NEGATIVE 273 79 36 46 3 NC_002967:TDE2722|5end_carhohydrate_kinase,_FGGY_family_2780874..2781104_NEGATIVE 273 80 34 196 129 NC_002967:TDE2429|5end_hypothetical_protein_2458037..2458267_NEGATIVE 273 57 20 65 28 NC_002967:TDE0389|5end_(R)-2-hydroxyglutaryl-CoA_dehydratase,_beta_subunit,_putative_440008..440238_POSITIVE 271 74 37 210 157 NC_002967:TDE1394|5end_hypothetical_protein_1433084..1433314_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 437 60 15 90 43 NC_002967:TDE2206|3end_hypothetical_protein_2244921..2245071_NEGATIVE 351 48 22 69 42 NC_002967:TDE2464|3end_hypothetical_protein_2489369..2489519_POSITIVE 332 75 50 26 1 NC_002967:TDE2000|3end_ABC_transporter,_ATP-binding/permease_protein,_HlyB_family_2019639..2019789_POSITIVE 327 63 21 67 11 NC_002967:TDE1072|3end_lipoprotein,_putative_1103436..1103586_POSITIVE 308 99 59 110 68 NC_002967:TDE1264|3end_hypothetical_protein_1298152..1298302_NEGATIVE 306 76 45 124 93 NC_002967:TDE1847|3end_hypothetical_protein_1875845..1875995_POSITIVE 299 80 35 147 88 NC_002967:TDE1521|3end_fumarate_hydratase_1567854..1568004_POSITIVE 295 78 37 139 97 NC_002967:TDE0597|3end_hypothetical_protein_636019..636169_NEGATIVE 291 75 35 147 110 NC_002967:TDE2725|3end_cyclic_nucleotide_binding_domain/GGDEF_domain_protein_2782240..2782390_NEGATIVE 291 79 37 55 1 NC_002967:TDE0452|3end_hypothetical_protein_509949..510099_NEGATIVE 290 59 19 114 61 NC_002967:TDE1099|3end_acetyltransferase,_GNAT_family_1133736..1133886_NEGATIVE 289 60 19 51 5 NC_002967:TDE0986|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1014121..1014271_POSITIVE 281 80 35 133 93 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 281 69 30 109 62 NC_002967:TDE1588|3end_tryptophanyl-tRNA_synthetase_1636966..1637116_POSITIVE 280 89 49 92 44 NC_002967:TDE0870|3end_phosphatase/nucleotidase_894676..894826_POSITIVE 275 100 59 77 45 NC_002967:TDE2656|3end_cobalt_chelatase_2693900..2694050_POSITIVE 273 79 36 49 6 NC_002967:TDE2723|3end_phosphoribosylpyrophosphate_synthetase_2780871..2781021_NEGATIVE 272 73 33 148 113 NC_002967:TDE2022|3end_YD_repeat_protein_2044756..2044906_NEGATIVE 265 61 21 85 43 NC_002967:TDE0792|3end_ribosomal_protein_L17_819006..819156_POSITIVE 262 76 36 151 126 NC_002967:TDE0408|3end_oxidoreductase,_NAD-binding_460536..460686_NEGATIVE