Origin IGS: attgtaaaccgagccttttgttaaacttaaggctcagaatatcacaaattcggtataataggaagaggttaaaattttaaaatcataaggagaaaagttttcagagcatttggctctgaaaacttaaagctctaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attagagctttaagttttcagagccaaatgctctgaaaacttttctccttatgattttaaaattttaacctcttcctattataccgaatttgtgatattctgagccttaagtttaacaaaaggctcggtttacaat Mask Tandem Repeat Region ================================================ attgtaaaccgagccttttgttaaacttaaggctcagaatatcacaaattcggtataataggaagaggttaaaattttaaaatcataaggagaaaagttttcagagcatttggctctgaaaacttaaagctctaat Find is-nt database================================================ Query_seq: TDE0639:TDE0640|TDE0639:TDE0640:oligopeptide/dipeptide ABC transporter, permease protein:methyl-accepting chemotaxis protein:<-<-:674485..674620 136 attgtaaaccgagccttttgttaaacttaaggctcagaatatcacaaattcggtataataggaagaggttaaaattttaaaatcataaggagaaaagttttcagagcatttggctctgaaaacttaaagctctaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0639:TDE0640|TDE0639:TDE0640:oligopeptide/dipeptide ABC transporter, permease protein:methyl-accepting chemotaxis protein:<-<-:674485..674620 136 attgtaaaccgagccttttgttaaacttaaggctcagaatatcacaaattcggtataataggaagaggttaaaattttaaaatcataaggagaaaagttttcagagcatttggctctgaaaacttaaagctctaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0639:TDE0640|TDE0639:TDE0640:oligopeptide/dipeptide ABC transporter, permease protein:methyl-accepting chemotaxis protein:<-<-:674485..674620 136 attgtaaaccgagccttttgttaaacttaaggctcagaatatcacaaattcggtataataggaagaggttaaaattttaaaatcataaggagaaaagttttcagagcatttggctctgaaaacttaaagctctaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attgtaaaccgagccttttgttaaacttaaggctcagaatatcacaaattcggtataataggaagaggttaaaattttaaaatcataaggagaaaagttttcagagcatttggctctgaaaacttaaagctctaat Predict ORF larger than 30AA ================================================ attgtaaaccgagccttttgttaaacttaaggctcagaatatcacaaattcggtataataggaagaggttaaaattttaaaatcataaggagaaaagttttcagagcatttggctctgaaaacttaaagctctaat 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================================================ attgtaaaccgagccttttgttaaacttaaggctcagaatatcacaaattcggtataataggaagaggttaaaattttaaaatcataaggagaaaagttttcagagcatttggctctgaaaacttaaagctctaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0639:TDE0640|TDE0639:TDE0640:oligopeptide/dipeptide ABC transporter, permease protein:methyl-accepting chemotaxis protein:<-<-:674485..674620 136 attgtaaaccgagccttttgttaaacttaaggctcagaatatcacaaattcggtataataggaagaggttaaaattttaaaatcataaggagaaaagttttcagagcatttggctctgaaaacttaaagctctaat Intra-Species Hit: Count: 1 Min: 1 Max: 136 Len: 136 Subject: NC_002967_TDE0639_TDE0640|oligopeptide/dipeptide ABC transporter, permease protein:methyl-accepting chemotaxis protein|NEGATIVE:NEGATIVE|[674485,674620]|136 HSP 1 e-value: 1.0E-71 bit: 270.0 Len: 136 Query Start:1 Query End:136 Subject Strand: POSITIVE Subject Start: 1 Subject End: 136 attgtaaaccgagccttttgttaaacttaaggctcagaatatcacaaattcggtataataggaagaggttaaaattttaaaatcataaggagaaaagttttcagagcatttggctctgaaaacttaaagctctaat attgtaaaccgagccttttgttaaacttaaggctcagaatatcacaaattcggtataataggaagaggttaaaattttaaaatcataaggagaaaagttttcagagcatttggctctgaaaacttaaagctctaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUGUAAACCGAGCCUUUUGUUAAACUUAAGGCUCAGAAUAUCACAAAUUCGGUAUAAUAGGAAGAGGUUAAAAUUUUAAAAUCAUAAGGAGAAAAGUUUUCAGAGCAUUUGGCUCUGAAAACUUAAAGCUCUAAU ((((((....(((((((..(.....)..))))))).((((.......))))..)))))).....((..((((....))))..))....((((..(((((((((((((.....)))))))))))))....))))... (-39.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAGAGCUUUAAGUUUUCAGAGCCAAAUGCUCUGAAAACUUUUCUCCUUAUGAUUUUAAAAUUUUAACCUCUUCCUAUUAUACCGAAUUUGUGAUAUUCUGAGCCUUAAGUUUAACAAAAGGCUCGGUUUACAAU ....(((....(((((((((((((.....)))))))))))))..)))..........................................((((((....(((((((((..(.....)..))))))))).)))))). (-37.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 801 130 81 221 172 NC_002967:TDE0639|5end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_674394..674624_NEGATIVE 298 45 1 216 170 NC_002967:TDE2634|5end_hypothetical_protein_2674625..2674855_POSITIVE 263 127 81 76 35 NC_002967:TDE2162|5end_NOL1/NOP2/sun_family_protein_2194689..2194919_POSITIVE 233 43 2 220 179 NC_002967:TDE1160|5end_hypothetical_protein_1195841..1196071_NEGATIVE 228 80 31 75 35 NC_002967:TDE0986|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1013061..1013291_POSITIVE 228 55 11 70 16 NC_002967:TDE0599|5end_PIN_domain_protein_638577..638807_NEGATIVE 226 118 101 144 126 NC_002967:TDE2225|5end_thioesterase_family_protein_2264868..2265098_POSITIVE 226 118 101 19 1 NC_002967:TDE2224|5end_hypothetical_protein_2264743..2264973_POSITIVE 226 118 101 144 126 NC_002967:TDE1132|5end_chorismate_synthase_1163415..1163645_POSITIVE 221 69 29 154 121 NC_002967:TDE2111|5end_hypothetical_protein_2137185..2137415_NEGATIVE 217 125 83 146 88 NC_002967:TDE2574|5end_conserved_hypothetical_protein_TIGR00650_2600376..2600606_POSITIVE 215 125 86 222 174 NC_002967:TDE1143|5end_hypothetical_protein_1181834..1182064_NEGATIVE 209 32 4 176 142 NC_002967:TDE1883|5end_hypothetical_protein_1905842..1906072_NEGATIVE 208 60 11 167 131 NC_002967:TDE1108|5end_hypothetical_protein_1142859..1143089_NEGATIVE 206 60 14 173 123 NC_002967:TDE2020|5end_YD_repeat_protein_2044156..2044386_NEGATIVE 206 130 82 190 129 NC_002967:TDE1081|5end_hypothetical_protein_1112639..1112869_POSITIVE 206 55 11 133 95 NC_002967:TDE0137|5end_carbohydrate_kinase,_FGGY_family_156640..156870_POSITIVE 205 130 88 47 8 NC_002967:TDE2109|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_2135287..2135517_NEGATIVE 203 55 13 224 183 NC_002967:TDE2618|5end_PHP_domain_protein_2659392..2659622_POSITIVE 203 113 93 139 115 NC_002967:TDE0242|5end_hypothetical_protein_276024..276254_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 260 48 2 69 24 NC_002967:TDE2336|3end_sodium/dicarboxylate_symporter_family_protein_2371925..2372075_NEGATIVE 237 127 96 31 4 NC_002967:TDE2161|3end_acetyltransferase,_GNAT_family_2194724..2194874_POSITIVE 228 55 11 85 31 NC_002967:TDE0600|3end_hypothetical_protein_638562..638712_NEGATIVE 226 118 101 147 129 NC_002967:TDE2224|3end_hypothetical_protein_2264951..2265101_POSITIVE 226 118 101 22 4 NC_002967:TDE2223|3end_hypothetical_protein_2264826..2264976_POSITIVE 217 125 83 149 91 NC_002967:TDE2573|3end_glucose-6-phosphate_isomerase_2600459..2600609_POSITIVE 213 129 88 88 42 NC_002967:TDE0926|3end_phosphonate_ABC_transporter,_permease_protein,_putative_949192..949342_NEGATIVE 210 44 1 65 20 NC_002967:TDE2029|3end_hydrolase,_TatD_family_2057148..2057298_NEGATIVE 210 38 10 73 34 NC_002967:TDE1355|3end_hypothetical_protein_1395527..1395677_POSITIVE 209 32 4 144 110 NC_002967:TDE1884|3end_hypothetical_protein_1905874..1906024_NEGATIVE 206 55 11 136 98 NC_002967:TDE0136|3end_hypothetical_protein_156723..156873_POSITIVE 204 124 103 30 9 NC_002967:TDE2111|3end_hypothetical_protein_2136271..2136421_NEGATIVE 204 57 12 117 73 NC_002967:TDE0359|3end_ABC_transporter,_ATP-binding/permease_protein_402193..402343_NEGATIVE 203 113 93 137 113 NC_002967:TDE0243|3end_ABC_transporter,_ATP-binding_protein_276026..276176_NEGATIVE 199 50 5 144 92 NC_002967:TDE0122|3end_dihydrouridine_synthase,_putative_140526..140676_NEGATIVE 198 71 31 146 104 NC_002967:TDE2507|3end_hypothetical_protein_2531643..2531793_NEGATIVE 197 84 44 74 36 NC_002967:TDE1435|3end_hypothetical_protein_1479543..1479693_POSITIVE 197 70 26 127 60 NC_002967:TDE0984|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein,_putative_1011053..1011203_POSITIVE 196 68 52 21 5 NC_002967:TDE2319|3end_hypothetical_protein_2355835..2355985_NEGATIVE 196 124 98 109 75 NC_002967:TDE1525|3end_hypothetical_protein_1570654..1570804_POSITIVE