Origin IGS: actcatctcctatcgcataattaatacaaacaattatatcatagtttttgcagaaggtaaatttatttttttaaaatatcgcgccgccttgaatacaaaaagaatctaaagtataatctttaaaaagtttttttgcggggggattata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tataatccccccgcaaaaaaactttttaaagattatactttagattctttttgtattcaaggcggcgcgatattttaaaaaaataaatttaccttctgcaaaaactatgatataattgtttgtattaattatgcgataggagatgagt Mask Tandem Repeat Region ================================================ actcatctcctatcgcataattaatacaaacaattatatcatagtttttgcagaaggtaaatttatttttttaaaatatcgcgccgccttgaatacaaaaagaatctaaagtataatctttaaaaagtttttttgcggggggattata Find is-nt database================================================ Query_seq: TDE2207:TDE2208|TDE2207:TDE2208:hypothetical protein:conserved hypothetical protein TIGR00486:<-->:2246725..2246872 148 actcatctcctatcgcataattaatacaaacaattatatcatagtttttgcagaaggtaaatttatttttttaaaatatcgcgccgccttgaatacaaaaagaatctaaagtataatctttaaaaagtttttttgcggggggattata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2207:TDE2208|TDE2207:TDE2208:hypothetical protein:conserved hypothetical protein TIGR00486:<-->:2246725..2246872 148 actcatctcctatcgcataattaatacaaacaattatatcatagtttttgcagaaggtaaatttatttttttaaaatatcgcgccgccttgaatacaaaaagaatctaaagtataatctttaaaaagtttttttgcggggggattata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2207:TDE2208|TDE2207:TDE2208:hypothetical protein:conserved hypothetical protein TIGR00486:<-->:2246725..2246872 148 actcatctcctatcgcataattaatacaaacaattatatcatagtttttgcagaaggtaaatttatttttttaaaatatcgcgccgccttgaatacaaaaagaatctaaagtataatctttaaaaagtttttttgcggggggattata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actcatctcctatcgcataattaatacaaacaattatatcatagtttttgcagaaggtaaatttatttttttaaaatatcgcgccgccttgaatacaaaaagaatctaaagtataatctttaaaaagtttttttgcggggggattata Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 5 End: 106 .... M S Y R I I N T N N Y I I V F A E G K F I F L K Y R A A L N T K R I .......................................... actcatctcctatcgcataattaatacaaacaattatatcatagtttttgcagaaggtaaatttatttttttaaaatatcgcgccgccttgaatacaaaaagaatctaaagtataatctttaaaaagtttttttgcggggggattata 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: 88 End: 117 .......................................................................................CTTGAATACAAAAAGAATCTAAAGTATAAT............................... PromScan Matrix: RpoD-17 Strand: - Score: 85 Start: 33 End: 62 ................................ATTTACCTTCTGCAAAAACTATGATATAAT...................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ actcatctcctatcgcataattaatacaaacaattatatcatagtttttgcagaaggtaaatttatttttttaaaatatcgcgccgccttgaatacaaaaagaatctaaagtataatctttaaaaagtttttttgcggggggattata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2207:TDE2208|TDE2207:TDE2208:hypothetical protein:conserved hypothetical protein TIGR00486:<-->:2246725..2246872 148 actcatctcctatcgcataattaatacaaacaattatatcatagtttttgcagaaggtaaatttatttttttaaaatatcgcgccgccttgaatacaaaaagaatctaaagtataatctttaaaaagtttttttgcggggggattata Intra-Species Hit: Count: 1 Min: 1 Max: 127 Len: 127 Subject: NC_002967_TDE2207_TDE2208|hypothetical protein:conserved hypothetical protein TIGR00486|NEGATIVE:POSITIVE|[2246725,2246872]|148 HSP 1 e-value: 9.0E-54 bit: 210.0 Len: 127 Query Start:1 Query End:127 Subject Strand: POSITIVE Subject Start: 1 Subject End: 127 actcatctcctatcgcataattaatacaaacaattatatcatagtttttgcagaaggtaaatttannnnnnnaaaatatcgcgccgccttgaatacaaaaagaatctaaagtataatctttaaaaag..................... actcatctcctatcgcataattaatacaaacaattatatcatagtttttgcagaaggtaaatttatttttttaaaatatcgcgccgccttgaatacaaaaagaatctaaagtataatctttaaaaag..................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUCAUCUCCUAUCGCAUAAUUAAUACAAACAAUUAUAUCAUAGUUUUUGCAGAAGGUAAAUUUAUUUUUUUAAAAUAUCGCGCCGCCUUGAAUACAAAAAGAAUCUAAAGUAUAAUCUUUAAAAAG ................................(((((((..(((((((((...(((((.....(((((.....))))).......))))).....))))))....)))..))))))).......... ( -9.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUUUAAAGAUUAUACUUUAGAUUCUUUUUGUAUUCAAGGCGGCGCGAUAUUUUAAAAAAAUAAAUUUACCUUCUGCAAAAACUAUGAUAUAAUUGUUUGUAUUAAUUAUGCGAUAGGAGAUGAGU ...(((((((......))))))).((((.((((((.....((((........((((......))))........))))........((((((((....))))))))...)))))).))))....... (-17.19) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 768 120 71 211 162 NC_002967:TDE2207|5end_hypothetical_protein_2246634..2246864_NEGATIVE 276 118 73 215 165 NC_002967:TDE0925|5end_peptidase_T_947847..948077_POSITIVE 251 91 52 119 80 NC_002967:TDE1291|5end_HD_domain_protein_1329213..1329443_NEGATIVE 240 88 43 231 185 NC_002967:TDE1588|5end_tryptophanyl-tRNA_synthetase_1635813..1636043_POSITIVE 236 98 76 112 90 NC_002967:TDE0220|5end_hypothetical_protein_254005..254235_NEGATIVE 234 114 82 218 183 NC_002967:TDE0545|5end_hypothetical_protein_584774..585004_POSITIVE 233 88 45 40 1 NC_002967:TDE0349|5end_phosphoenolpyruvate_synthase,_putative_391093..391323_POSITIVE 221 89 43 64 24 NC_002967:TDE2586|5end_DNA_polymerase_III_subunits_gamma_and_tau_2622089..2622319_NEGATIVE 221 88 45 229 178 NC_002967:TDE0834|5end_Na(+)-translocating_NADH-quinone_reductase,_E_subunit_854863..855093_NEGATIVE 221 118 81 43 15 NC_002967:TDE0143|5end_thiamine_ABC_transporter,_thiamine-binding_protein_164013..164243_POSITIVE 220 91 53 72 33 NC_002967:TDE2559|5end_ABC_transporter,_ATP-binding/permease_protein_2587204..2587434_NEGATIVE 219 96 56 131 81 NC_002967:TDE1093|5end_hypothetical_protein_1127374..1127604_POSITIVE 215 90 50 225 178 NC_002967:TDE2042|5end_hypothetical_protein_2072179..2072409_NEGATIVE 212 103 73 57 33 NC_002967:TDE1077|5end_hypothetical_protein_1108395..1108625_POSITIVE 206 43 1 111 65 NC_002967:TDE0713|5end_transcription_antitermination_protein,_NusG_family_747109..747339_POSITIVE 204 90 43 193 139 NC_002967:TDE0921|5end_ABC_transporter,_ATP-binding/permease_protein_941857..942087_NEGATIVE 201 96 59 210 167 NC_002967:TDE0851|5end_hypothetical_protein_874997..875227_NEGATIVE 199 96 82 123 109 NC_002967:TDE2491|5end_DNA_polymerase_domain_protein_2515499..2515729_NEGATIVE 199 108 61 151 101 NC_002967:TDE0321|5end_CBS_domain_protein_355094..355324_NEGATIVE 196 92 80 210 198 NC_002967:TDE0946|5end_hypothetical_protein_968212..968442_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 245 90 55 144 97 NC_002967:TDE1221|3end_glycosyl_hydrolase,_family_3_1256078..1256228_POSITIVE 236 98 76 71 49 NC_002967:TDE0221|3end_hypothetical_protein_254046..254196_NEGATIVE 217 116 81 68 32 NC_002967:TDE0745|3end_glycine_reductase_complex_selenoprotein_GrdA_780840..780990_POSITIVE 213 89 43 130 74 NC_002967:TDE0038|3end_3-oxoacyl-(acyl-carrier-protein)_synthase_II_43036..43186_NEGATIVE 209 87 48 137 99 NC_002967:TDE0761|3end_protease_complex-associated_polypeptide_801968..802118_POSITIVE 208 89 41 151 94 NC_002967:TDE2665|3end_inositol-5-monophosphate_dehydrogenase_2703611..2703761_POSITIVE 205 89 42 110 65 NC_002967:TDE0185|3end_ABC_transporter,_ATP-binding_protein,_HlyB_family_222335..222485_POSITIVE 201 92 51 145 92 NC_002967:TDE2260|3end_hypothetical_protein_2297573..2297723_POSITIVE 199 96 82 113 99 NC_002967:TDE2492|3end_hypothetical_protein_2515509..2515659_NEGATIVE 199 108 61 139 89 NC_002967:TDE0322|3end_regulatory_protein,_P-II_family_355106..355256_NEGATIVE 198 58 15 76 40 NC_002967:TDE2254|3end_hypothetical_protein_2291445..2291595_NEGATIVE 198 88 45 68 26 NC_002967:TDE0353|3end_lipase/acylhydrolase,_GDSL_family_396743..396893_NEGATIVE 193 88 45 144 112 NC_002967:TDE1121|3end_hypothetical_protein_1152814..1152964_NEGATIVE 192 109 82 26 3 NC_002967:TDE2436|3end_hypothetical_protein_2467446..2467596_POSITIVE 192 90 45 53 5 NC_002967:TDE1067|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1094544..1094694_NEGATIVE 188 85 41 105 61 NC_002967:TDE0680|3end_protein-export_membrane_protein_SecF_717613..717763_NEGATIVE 186 87 45 137 101 NC_002967:TDE1898|3end_translocase_1918122..1918272_NEGATIVE 186 106 64 117 75 NC_002967:TDE0334|3end_hypothetical_protein_373296..373446_NEGATIVE 184 111 82 76 43 NC_002967:TDE2214|3end_hypothetical_protein_2253465..2253615_POSITIVE 184 96 76 122 101 NC_002967:TDE0210|3end_cob(I)yrinic_acid_a,c-diamide_adenosyltransferase_246146..246296_POSITIVE