Origin IGS: ttaaaaatgtttgaagatttaacaatgcgggattccaaagggctgcaagtcctttggcagcgcgagtacaaccagcggagcttcaaggtaaaaagggatgggg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ccccatccctttttaccttgaagctccgctggttgtactcgcgctgccaaaggacttgcagccctttggaatcccgcattgttaaatcttcaaacatttttaa Mask Tandem Repeat Region ================================================ ttaaaaatgtttgaagatttaacaatgcgggattccaaagggctgcaagtcctttggcagcgcgagtacaaccagcggagcttcaaggtaaaaagggatgggg Find is-nt database================================================ Query_seq: TDE1981:TDE1982|TDE1981:TDE1982:hypothetical protein:hypothetical protein:-><-:1992498..1992600 103 ttaaaaatgtttgaagatttaacaatgcgggattccaaagggctgcaagtcctttggcagcgcgagtacaaccagcggagcttcaaggtaaaaagggatgggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1981:TDE1982|TDE1981:TDE1982:hypothetical protein:hypothetical protein:-><-:1992498..1992600 103 ttaaaaatgtttgaagatttaacaatgcgggattccaaagggctgcaagtcctttggcagcgcgagtacaaccagcggagcttcaaggtaaaaagggatgggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1981:TDE1982|TDE1981:TDE1982:hypothetical protein:hypothetical protein:-><-:1992498..1992600 103 ttaaaaatgtttgaagatttaacaatgcgggattccaaagggctgcaagtcctttggcagcgcgagtacaaccagcggagcttcaaggtaaaaagggatgggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttaaaaatgtttgaagatttaacaatgcgggattccaaagggctgcaagtcctttggcagcgcgagtacaaccagcggagcttcaaggtaaaaagggatgggg Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 7 End: 102 ...... M F E D L T M R D S K G L Q V L W Q R E Y N Q R S F K V K R D G . ttaaaaatgtttgaagatttaacaatgcgggattccaaagggctgcaagtcctttggcagcgcgagtacaaccagcggagcttcaaggtaaaaagggatgggg 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================================================ ttaaaaatgtttgaagatttaacaatgcgggattccaaagggctgcaagtcctttggcagcgcgagtacaaccagcggagcttcaaggtaaaaagggatgggg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1981:TDE1982|TDE1981:TDE1982:hypothetical protein:hypothetical protein:-><-:1992498..1992600 103 ttaaaaatgtttgaagatttaacaatgcgggattccaaagggctgcaagtcctttggcagcgcgagtacaaccagcggagcttcaaggtaaaaagggatgggg Intra-Species Hit: Count: 1 Min: 1 Max: 103 Len: 103 Subject: NC_002967_TDE1981_TDE1982|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[1992498,1992600]|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 ttaaaaatgtttgaagatttaacaatgcgggattccaaagggctgcaagtcctttggcagcgcgagtacaaccagcggagcttcaaggtaaaaagggatgggg ttaaaaatgtttgaagatttaacaatgcgggattccaaagggctgcaagtcctttggcagcgcgagtacaaccagcggagcttcaaggtaaaaagggatgggg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAAAAUGUUUGAAGAUUUAACAAUGCGGGAUUCCAAAGGGCUGCAAGUCCUUUGGCAGCGCGAGUACAACCAGCGGAGCUUCAAGGUAAAAAGGGAUGGGG .........(((((((.........(((.((...(((((((((.....)))))))))..((....))....)).)))...)))))))................ (-25.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCCAUCCCUUUUUACCUUGAAGCUCCGCUGGUUGUACUCGCGCUGCCAAAGGACUUGCAGCCCUUUGGAAUCCCGCAUUGUUAAAUCUUCAAACAUUUUUAA .................((((((...(((.((.....)).)))...(((((((.(.....).)))))))..................)))))).......... (-18.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 843 97 51 150 102 NC_002967:TDE2260|5end_hypothetical_protein_2297338..2297568_POSITIVE 501 76 33 41 1 NC_002967:TDE0827|5end_hypothetical_protein_848053..848283_NEGATIVE 493 64 28 200 165 NC_002967:TDE1060|5end_hypothetical_protein_1086519..1086749_POSITIVE 482 88 44 191 146 NC_002967:TDE2309|5end_sigma-54_dependent_transcriptional_regulator,_putative_2348099..2348329_NEGATIVE 459 63 28 231 195 NC_002967:TDE0403|5end_hypothetical_protein_454433..454663_POSITIVE 402 79 32 44 1 NC_002967:TDE1974|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_1988910..1989140_NEGATIVE 368 62 24 210 174 NC_002967:TDE2419|5end_hypothetical_protein_2444769..2444999_NEGATIVE 363 69 25 204 167 NC_002967:TDE0589|5end_acetyl-CoA_carboxylase,_carboxyl_transferase,_alpha_subunit_629044..629274_NEGATIVE 361 81 41 219 178 NC_002967:TDE1846|5end_hypothetical_protein_1875426..1875656_NEGATIVE 357 59 28 50 19 NC_002967:TDE0239|5end_glycine_reductase_complex_protein_GrdD_272982..273212_NEGATIVE 349 63 38 36 5 NC_002967:TDE1042|5end_deoxyuridine_5'triphosphate_nucleotidohydrolase_1070492..1070722_POSITIVE 344 68 22 63 12 NC_002967:TDE2554|5end_chaperonin,_33_kDa_family_2580745..2580975_POSITIVE 331 66 23 137 99 NC_002967:TDE0860|5end_ribosomal_small_subunit_pseudouridine_synthase_A_881023..881253_POSITIVE 326 63 22 94 51 NC_002967:TDE2103|5end_glycosyl_transferase,_group_2_family_protein_2128393..2128623_NEGATIVE 322 67 27 110 78 NC_002967:TDE2102|5end_hypothetical_protein_2127347..2127577_NEGATIVE 320 79 39 194 143 NC_002967:TDE1391|5end_NQR2/RnfD/RnfE_family_protein_1430975..1431205_POSITIVE 316 83 41 73 32 NC_002967:TDE2028|5end_OmpA_family_protein_2052923..2053153_POSITIVE 312 64 29 49 18 NC_002967:TDE2141|5end_hypothetical_protein_2175768..2175998_NEGATIVE 311 65 27 60 7 NC_002967:TDE0947|5end_translation_elongation_factor_G,_putative_970792..971022_NEGATIVE 308 89 41 69 16 NC_002967:TDE2517|5end_DNA_repair_protein_RadA_2543842..2544072_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 449 88 58 146 107 NC_002967:TDE2136|3end_hypothetical_protein_2165390..2165540_NEGATIVE 394 92 64 53 24 NC_002967:TDE1893|3end_GTP-binding_protein_LepA_1912212..1912362_NEGATIVE 370 74 31 134 94 NC_002967:TDE2205|3end_enoate_reductase,_putative_2242575..2242725_NEGATIVE 370 67 21 148 109 NC_002967:TDE1057|3end_hypothetical_protein_1086105..1086255_NEGATIVE 357 59 28 37 6 NC_002967:TDE0240|3end_glycine_reductase_complex_protein_GrdC_272995..273145_NEGATIVE 349 69 22 130 77 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 348 61 23 67 13 NC_002967:TDE0763|3end_hypothetical_protein_804234..804384_NEGATIVE 340 62 21 45 12 NC_002967:TDE1008|3end_flagellar_protein,_putative_1032806..1032956_POSITIVE 331 66 23 140 102 NC_002967:TDE0859|3end_hypothetical_protein_881106..881256_POSITIVE 328 68 27 138 82 NC_002967:TDE0860|3end_ribosomal_small_subunit_pseudouridine_synthase_A_881840..881990_POSITIVE 326 63 22 64 24 NC_002967:TDE1981|3end_hypothetical_protein_1992437..1992587_POSITIVE 316 83 41 68 27 NC_002967:TDE2027|3end_hypothetical_protein_2052998..2053148_POSITIVE 316 89 51 138 99 NC_002967:TDE1340|3end_ribosomal_5S_rRNA_E-loop_binding_protein_Ctc/L25/TL5_1377032..1377182_POSITIVE 308 87 41 61 20 NC_002967:TDE1967|3end_hypothetical_protein_1982533..1982683_POSITIVE 307 88 41 78 24 NC_002967:TDE0943|3end_hypothetical_protein_966272..966422_POSITIVE 306 82 41 112 77 NC_002967:TDE0616|3end_hypothetical_protein_650079..650229_POSITIVE 304 89 42 122 59 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 303 89 41 66 17 NC_002967:TDE2513|3end_glucose-inhibited_division_protein_B_2539888..2540038_POSITIVE 302 90 41 123 87 NC_002967:TDE0572|3end_hypothetical_protein_604734..604884_POSITIVE 301 58 24 130 85 NC_002967:TDE2126|3end_hypothetical_protein_2159843..2159993_POSITIVE