Origin IGS: ccggctttaaagccgggctctaaagccaatttttattagccggtaagcgatgtttaccggctttgccgagagatgtccttatagttattttgtaacgttaacttaatctttgtgtttttacaaacgcttaatttggagaatcctatggctaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttagccataggattctccaaattaagcgtttgtaaaaacacaaagattaagttaacgttacaaaataactataaggacatctctcggcaaagccggtaaacatcgcttaccggctaataaaaattggctttagagcccggctttaaagccgg Mask Tandem Repeat Region ================================================ ccggctttaaagccgggctctaaagccaatttttattagccggtaagcgatgtttaccggctttgccgagagatgtccttatagttattttgtaacgttaacttaatctttgtgtttttacaaacgcttaatttggagaatcctatggctaaa Find is-nt database================================================ Query_seq: TDE0845:TDE0846|TDE0845:TDE0846:conserved hypothetical protein TIGR00266:hypothetical protein:->->:868610..868762 153 ccggctttaaagccgggctctaaagccaatttttattagccggtaagcgatgtttaccggctttgccgagagatgtccttatagttattttgtaacgttaacttaatctttgtgtttttacaaacgcttaatttggagaatcctatggctaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0845:TDE0846|TDE0845:TDE0846:conserved hypothetical protein TIGR00266:hypothetical protein:->->:868610..868762 153 ccggctttaaagccgggctctaaagccaatttttattagccggtaagcgatgtttaccggctttgccgagagatgtccttatagttattttgtaacgttaacttaatctttgtgtttttacaaacgcttaatttggagaatcctatggctaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0845:TDE0846|TDE0845:TDE0846:conserved hypothetical protein TIGR00266:hypothetical protein:->->:868610..868762 153 ccggctttaaagccgggctctaaagccaatttttattagccggtaagcgatgtttaccggctttgccgagagatgtccttatagttattttgtaacgttaacttaatctttgtgtttttacaaacgcttaatttggagaatcctatggctaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ccggctttaaagccgggctctaaagccaatttttattagccggtaagcgatgtttaccggctttgccgagagatgtccttatagttattttgtaacgttaacttaatctttgtgtttttacaaacgcttaatttggagaatcctatggctaaa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 57 End: 146 ........................................................ R S Q R S I D K Y N N Q L T L K I K T N K C V S L K S F G M ....... ccggctttaaagccgggctctaaagccaatttttattagccggtaagcgatgtttaccggctttgccgagagatgtccttatagttattttgtaacgttaacttaatctttgtgtttttacaaacgcttaatttggagaatcctatggctaaa 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================================================ ccggctttaaagccgggctctaaagccaatttttattagccggtaagcgatgtttaccggctttgccgagagatgtccttatagttattttgtaacgttaacttaatctttgtgtttttacaaacgcttaatttggagaatcctatggctaaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -14.2 Tail_Score: -3.53563 Start: 39 End: 61 Full_Region: AGCCAATTTTTATTA GCCGGTAAGC GAT GTTTACCGGC TTTGCCGAGAGATGT ......................................GCCGGTAAGCGATGTTTACCGGC............................................................................................ Find igs database================================================ Query_seq: TDE0845:TDE0846|TDE0845:TDE0846:conserved hypothetical protein TIGR00266:hypothetical protein:->->:868610..868762 153 ccggctttaaagccgggctctaaagccaatttttattagccggtaagcgatgtttaccggctttgccgagagatgtccttatagttattttgtaacgttaacttaatctttgtgtttttacaaacgcttaatttggagaatcctatggctaaa Intra-Species Hit: Count: 1 Min: 1 Max: 153 Len: 153 Subject: NC_002967_TDE0845_TDE0846|conserved hypothetical protein TIGR00266:hypothetical protein|POSITIVE:POSITIVE|[868610,868762]|153 HSP 1 e-value: 9.0E-82 bit: 303.0 Len: 153 Query Start:1 Query End:153 Subject Strand: POSITIVE Subject Start: 1 Subject End: 153 ccggctttaaagccgggctctaaagccaatttttattagccggtaagcgatgtttaccggctttgccgagagatgtccttatagttattttgtaacgttaacttaatctttgtgtttttacaaacgcttaatttggagaatcctatggctaaa ccggctttaaagccgggctctaaagccaatttttattagccggtaagcgatgtttaccggctttgccgagagatgtccttatagttattttgtaacgttaacttaatctttgtgtttttacaaacgcttaatttggagaatcctatggctaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCGGCUUUAAAGCCGGGCUCUAAAGCCAAUUUUUAUUAGCCGGUAAGCGAUGUUUACCGGCUUUGCCGAGAGAUGUCCUUAUAGUUAUUUUGUAACGUUAACUUAAUCUUUGUGUUUUUACAAACGCUUAAUUUGGAGAAUCCUAUGGCUAAA ..(((((((.(((...))).)))))))..........(((((((((((...)))))))))))..((((((.(((.(((.....(((((...)))))...............((((((....)))))).......)))..))))).)))).... (-45.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAGCCAUAGGAUUCUCCAAAUUAAGCGUUUGUAAAAACACAAAGAUUAAGUUAACGUUACAAAAUAACUAUAAGGACAUCUCUCGGCAAAGCCGGUAAACAUCGCUUACCGGCUAAUAAAAAUUGGCUUUAGAGCCCGGCUUUAAAGCCGG ....(((...((((..(((.......(.((((....)))).)........(((((...........)))))....))).))))...)))..(((((((((.......))))))))).........((((((((((((...)))))))))))). (-43.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 344 70 32 207 170 NC_002967:TDE2101|5end_hypothetical_protein_2126619..2126849_NEGATIVE 344 50 2 111 47 NC_002967:TDE1951|5end_ribonuclease_Z_1968329..1968559_NEGATIVE 336 84 41 60 11 NC_002967:TDE2151|5end_hypothetical_protein_2188807..2189037_NEGATIVE 332 68 30 108 69 NC_002967:TDE1139|5end_hypothetical_protein_1168615..1168845_NEGATIVE 322 78 37 129 73 NC_002967:TDE1884|5end_hypothetical_protein_1906857..1907087_NEGATIVE 321 60 11 67 15 NC_002967:TDE0872|5end_recA_protein_894841..895071_POSITIVE 319 42 1 168 135 NC_002967:TDE0601|5end_malonyl_CoA-acyl_carrier_protein_transacylase,_putative_639811..640041_NEGATIVE 312 60 11 130 77 NC_002967:TDE2516|5end_hypothetical_protein_2542021..2542251_POSITIVE 310 42 1 203 150 NC_002967:TDE2607|5end_hypothetical_protein_2648586..2648816_POSITIVE 310 45 1 107 69 NC_002967:TDE0946|5end_hypothetical_protein_968212..968442_POSITIVE 305 77 39 180 136 NC_002967:TDE2404|5end_RNA_polymerase_sigma-54_factor,_putative_2430704..2430934_NEGATIVE 305 68 23 231 191 NC_002967:TDE2042|5end_hypothetical_protein_2072179..2072409_NEGATIVE 303 29 1 91 69 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 303 50 2 196 140 NC_002967:TDE1261|5end_choline/carnitine/betaine_transporter_family_protein_1295593..1295823_POSITIVE 299 49 1 126 63 NC_002967:TDE2731|5end_TIM-barrel_protein,_putative,_NifR3_family_2787372..2787602_POSITIVE 297 78 39 218 174 NC_002967:TDE2061|5end_hypothetical_protein_2087792..2088022_NEGATIVE 296 46 1 79 39 NC_002967:TDE1175|5end_chaperonin_GroEL_1205151..1205381_NEGATIVE 293 60 11 82 26 NC_002967:TDE2548|5end_hypothetical_protein_2573198..2573428_NEGATIVE 293 60 13 216 166 NC_002967:TDE0691|5end_ABC_transporter,_ATP-binding/permease_protein_728062..728292_POSITIVE 292 87 41 71 8 NC_002967:TDE0628|5end_molecular_chaperone_DnaK_660609..660839_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 363 49 1 118 65 NC_002967:TDE2422|3end_ribosomal_protein_L7/L12_2452911..2453061_NEGATIVE 345 80 39 132 96 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 337 62 38 53 29 NC_002967:TDE0845|3end_conserved_hypothetical_protein_TIGR00266_868549..868699_POSITIVE 336 84 41 63 14 NC_002967:TDE2152|3end_hypothetical_protein_2188804..2188954_NEGATIVE 329 80 39 132 96 NC_002967:TDE2515|3end_hypothetical_protein_2540972..2541122_NEGATIVE 321 49 3 147 95 NC_002967:TDE1056|3end_hypothetical_protein_1085895..1086045_POSITIVE 319 42 1 143 110 NC_002967:TDE0602|3end_3-oxoacyl-(acyl-carrier-protein)_synthase_III_639836..639986_NEGATIVE 316 61 22 70 25 NC_002967:TDE1003|3end_hypothetical_protein_1029325..1029475_POSITIVE 310 42 1 88 35 NC_002967:TDE2606|3end_urocanate_hydratase_2648551..2648701_POSITIVE 310 45 1 135 97 NC_002967:TDE0945|3end_hypothetical_protein_968320..968470_POSITIVE 303 29 1 119 97 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 299 49 1 113 50 NC_002967:TDE2730|3end_hydrolase,_TatD_family_2787439..2787589_POSITIVE 295 88 41 129 81 NC_002967:TDE2571|3end_hypothetical_protein_2597922..2598072_NEGATIVE 295 73 39 58 6 NC_002967:TDE0143|3end_thiamine_ABC_transporter,_thiamine-binding_protein_165103..165253_POSITIVE 291 80 39 49 16 NC_002967:TDE2209|3end_CarB_family_protein_2249300..2249450_POSITIVE 291 48 3 52 14 NC_002967:TDE1911|3end_hypothetical_protein_1928943..1929093_NEGATIVE 291 79 38 148 108 NC_002967:TDE0038|3end_3-oxoacyl-(acyl-carrier-protein)_synthase_II_43036..43186_NEGATIVE 286 49 1 148 97 NC_002967:TDE2101|3end_hypothetical_protein_2125549..2125699_NEGATIVE 286 44 1 58 26 NC_002967:TDE1384|3end_cadmium-translocating_P-type_ATPase_1424776..1424926_POSITIVE 286 80 32 136 90 NC_002967:TDE0448|3end_deoxyribose-phosphate_aldolase_506526..506676_POSITIVE