Origin IGS: ttatcagcctattttaactttatgcagcttgcagcagcaggctgctaacctcggcttgactatgaggccttaaacgattaaaataaacgcatacaatttgttttaaggagttttaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttaaaactccttaaaacaaattgtatgcgtttattttaatcgtttaaggcctcatagtcaagccgaggttagcagcctgctgctgcaagctgcataaagttaaaataggctgataa Mask Tandem Repeat Region ================================================ ttatcagcctattttaactttatgcagcttgcagcagcaggctgctaacctcggcttgactatgaggccttaaacgattaaaataaacgcatacaatttgttttaaggagttttaa Find is-nt database================================================ Query_seq: TDE2068:TDE2069|TDE2068:TDE2069:antigen, putative:endoribonuclease L-PSP, putative:->->:2096656..2096771 116 ttatcagcctattttaactttatgcagcttgcagcagcaggctgctaacctcggcttgactatgaggccttaaacgattaaaataaacgcatacaatttgttttaaggagttttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2068:TDE2069|TDE2068:TDE2069:antigen, putative:endoribonuclease L-PSP, putative:->->:2096656..2096771 116 ttatcagcctattttaactttatgcagcttgcagcagcaggctgctaacctcggcttgactatgaggccttaaacgattaaaataaacgcatacaatttgttttaaggagttttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2068:TDE2069|TDE2068:TDE2069:antigen, putative:endoribonuclease L-PSP, putative:->->:2096656..2096771 116 ttatcagcctattttaactttatgcagcttgcagcagcaggctgctaacctcggcttgactatgaggccttaaacgattaaaataaacgcatacaatttgttttaaggagttttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttatcagcctattttaactttatgcagcttgcagcagcaggctgctaacctcggcttgactatgaggccttaaacgattaaaataaacgcatacaatttgttttaaggagttttaa Predict ORF larger than 30AA ================================================ ttatcagcctattttaactttatgcagcttgcagcagcaggctgctaacctcggcttgactatgaggccttaaacgattaaaataaacgcatacaatttgttttaaggagttttaa 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: 86 Start: 55 End: 84 ......................................................CTTGACTATGAGGCCTTAAACGATTAAAAT................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttatcagcctattttaactttatgcagcttgcagcagcaggctgctaacctcggcttgactatgaggccttaaacgattaaaataaacgcatacaatttgttttaaggagttttaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2068:TDE2069|TDE2068:TDE2069:antigen, putative:endoribonuclease L-PSP, putative:->->:2096656..2096771 116 ttatcagcctattttaactttatgcagcttgcagcagcaggctgctaacctcggcttgactatgaggccttaaacgattaaaataaacgcatacaatttgttttaaggagttttaa Intra-Species Hit: Count: 1 Min: 1 Max: 116 Len: 116 Subject: NC_002967_TDE2068_TDE2069|antigen, putative:endoribonuclease L-PSP, putative|POSITIVE:POSITIVE|[2096656,2096771]|116 HSP 1 e-value: 8.0E-60 bit: 230.0 Len: 116 Query Start:1 Query End:116 Subject Strand: POSITIVE Subject Start: 1 Subject End: 116 ttatcagcctattttaactttatgcagcttgcagcagcaggctgctaacctcggcttgactatgaggccttaaacgattaaaataaacgcatacaatttgttttaaggagttttaa ttatcagcctattttaactttatgcagcttgcagcagcaggctgctaacctcggcttgactatgaggccttaaacgattaaaataaacgcatacaatttgttttaaggagttttaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUCAGCCUAUUUUAACUUUAUGCAGCUUGCAGCAGCAGGCUGCUAACCUCGGCUUGACUAUGAGGCCUUAAACGAUUAAAAUAAACGCAUACAAUUUGUUUUAAGGAGUUUUAA .......................(((((((((....))))))))).......(((((.......)))))..((((..((((((((((.........))))))))))...))))... (-27.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAAACUCCUUAAAACAAAUUGUAUGCGUUUAUUUUAAUCGUUUAAGGCCUCAUAGUCAAGCCGAGGUUAGCAGCCUGCUGCUGCAAGCUGCAUAAAGUUAAAAUAGGCUGAUAA ............................((((((((((((.......((((((...........)))))).(((((.(((....))).))))).....))))))))))))...... (-28.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 416 69 23 113 61 NC_002967:TDE2515|5end_hypothetical_protein_2542057..2542287_NEGATIVE 382 69 23 120 74 NC_002967:TDE2103|5end_glycosyl_transferase,_group_2_family_protein_2128393..2128623_NEGATIVE 366 69 24 70 10 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 364 69 31 41 4 NC_002967:TDE0572|5end_hypothetical_protein_603494..603724_POSITIVE 348 63 26 175 141 NC_002967:TDE0134|5end_oxidoreductase,_FAD-dependent_153404..153634_POSITIVE 342 69 24 97 39 NC_002967:TDE2209|5end_CarB_family_protein_2247589..2247819_POSITIVE 339 68 25 196 152 NC_002967:TDE2251|5end_uracil_permease_2289440..2289670_POSITIVE 339 80 34 75 36 NC_002967:TDE0153|5end_coenzyme_A_disulfide_reductase,_putative_176185..176415_NEGATIVE 337 70 23 197 158 NC_002967:TDE1056|5end_hypothetical_protein_1085210..1085440_POSITIVE 335 60 11 153 93 NC_002967:TDE1803|5end_hypothetical_protein_1839270..1839500_NEGATIVE 331 69 23 188 129 NC_002967:TDE2632|5end_peptide_ABC_transporter,_ATP-binding_protein,_putative_2672650..2672880_POSITIVE 330 55 15 187 139 NC_002967:TDE1769|5end_hypothetical_protein_1814377..1814607_NEGATIVE 328 46 3 215 173 NC_002967:TDE2661|5end_hypothetical_protein_2697772..2698002_NEGATIVE 324 68 26 76 19 NC_002967:TDE2731|5end_TIM-barrel_protein,_putative,_NifR3_family_2787372..2787602_POSITIVE 323 68 26 149 95 NC_002967:TDE2516|5end_hypothetical_protein_2542021..2542251_POSITIVE 322 58 23 36 5 NC_002967:TDE2461|5end_selenide,_water_dikinase_(selenocysteine-containing)_2488260..2488490_NEGATIVE 317 69 21 76 29 NC_002967:TDE0084|5end_phosphoenolpyruvate-protein_phosphotransferase_97455..97685_NEGATIVE 314 70 31 170 136 NC_002967:TDE1863|5end_Holliday_junction_DNA_helicase_RuvA_1888579..1888809_NEGATIVE 313 57 19 229 195 NC_002967:TDE1127|5end_TPR_domain_protein_1158278..1158508_POSITIVE 312 79 33 192 133 NC_002967:TDE2428|5end_ribosomal_protein_L33_2456292..2456522_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 374 63 26 108 66 NC_002967:TDE1450|3end_MutS2_family_protein_1497856..1498006_POSITIVE 366 69 24 98 38 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 363 63 24 94 46 NC_002967:TDE2068|3end_antigen,_putative_2096595..2096745_POSITIVE 339 68 25 85 41 NC_002967:TDE2250|3end_hypothetical_protein_2289409..2289559_POSITIVE 339 80 34 52 13 NC_002967:TDE0154|3end_adenylate/guanylate_cyclase_catalytic_domain_protein_176208..176358_NEGATIVE 333 68 27 135 88 NC_002967:TDE0742|3end_hypothetical_protein_778450..778600_NEGATIVE 333 70 26 89 44 NC_002967:TDE0266|3end_hypothetical_protein_297767..297917_NEGATIVE 325 67 25 49 1 NC_002967:TDE0617|3end_hypothetical_protein_650093..650243_NEGATIVE 324 68 26 63 6 NC_002967:TDE2730|3end_hydrolase,_TatD_family_2787439..2787589_POSITIVE 320 70 26 99 53 NC_002967:TDE1691|3end_hypothetical_protein_1747407..1747557_NEGATIVE 317 68 24 67 12 NC_002967:TDE0763|3end_hypothetical_protein_804234..804384_NEGATIVE 308 69 28 52 16 NC_002967:TDE0452|3end_hypothetical_protein_509949..510099_NEGATIVE 300 68 22 54 9 NC_002967:TDE2104|3end_hypothetical_protein_2128525..2128675_NEGATIVE 300 78 31 61 15 NC_002967:TDE0134|3end_oxidoreductase,_FAD-dependent_155010..155160_POSITIVE 299 67 23 69 27 NC_002967:TDE1893|3end_GTP-binding_protein_LepA_1912212..1912362_NEGATIVE 298 51 19 122 90 NC_002967:TDE2617|3end_cyclic_nucleotide-binding_protein_2658343..2658493_NEGATIVE 298 60 17 78 31 NC_002967:TDE0781|3end_30S_ribosomal_protein_S8_813039..813189_POSITIVE 296 70 23 57 1 NC_002967:TDE2682|3end_hypothetical_protein_2721388..2721538_NEGATIVE 294 70 24 110 57 NC_002967:TDE0135|3end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_156377..156527_POSITIVE 291 70 23 66 6 NC_002967:TDE2763|3end_flagellar_motor_switch_protein_2817737..2817887_NEGATIVE