Origin IGS: ttgttatacaccttatttatttgtattatattttaaattaaaaaactagcggatctatgagagcgtccaactaatattctttcttaaacagatgaattttctgcttcacgaatacaaatccctttttttatattcaaatacattcctgtttgtattg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 caatacaaacaggaatgtatttgaatataaaaaaagggatttgtattcgtgaagcagaaaattcatctgtttaagaaagaatattagttggacgctctcatagatccgctagttttttaatttaaaatataatacaaataaataaggtgtataacaa Mask Tandem Repeat Region ================================================ ttgttatacaccttatttatttgtattatattttaaattaaaaaactagcggatctatgagagcgtccaactaatattctttcttaaacagatgaattttctgcttcacgaatacaaatccctttttttatattcaaatacattcctgtttgtattg Find is-nt database================================================ Query_seq: TDE0269:TDE0270|TDE0269:TDE0270:hypothetical protein:hypothetical protein:<-<-:300778..300934 157 ttgttatacaccttatttatttgtattatattttaaattaaaaaactagcggatctatgagagcgtccaactaatattctttcttaaacagatgaattttctgcttcacgaatacaaatccctttttttatattcaaatacattcctgtttgtattg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0269:TDE0270|TDE0269:TDE0270:hypothetical protein:hypothetical protein:<-<-:300778..300934 157 ttgttatacaccttatttatttgtattatattttaaattaaaaaactagcggatctatgagagcgtccaactaatattctttcttaaacagatgaattttctgcttcacgaatacaaatccctttttttatattcaaatacattcctgtttgtattg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0269:TDE0270|TDE0269:TDE0270:hypothetical protein:hypothetical protein:<-<-:300778..300934 157 ttgttatacaccttatttatttgtattatattttaaattaaaaaactagcggatctatgagagcgtccaactaatattctttcttaaacagatgaattttctgcttcacgaatacaaatccctttttttatattcaaatacattcctgtttgtattg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgttatacaccttatttatttgtattatattttaaattaaaaaactagcggatctatgagagcgtccaactaatattctttcttaaacagatgaattttctgcttcacgaatacaaatccctttttttatattcaaatacattcctgtttgtattg Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 53 End: 157 .................................................... M Y E S V Q L I F F L K Q M N F L L H E Y K S L F L Y S N T F L F V L ttgttatacaccttatttatttgtattatattttaaattaaaaaactagcggatctatgagagcgtccaactaatattctttcttaaacagatgaattttctgcttcacgaatacaaatccctttttttatattcaaatacattcctgtttgtattg 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: 85 Start: 0 End: 29 aTTGTTATACACCTTATTTATTTGTATTAT................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttgttatacaccttatttatttgtattatattttaaattaaaaaactagcggatctatgagagcgtccaactaatattctttcttaaacagatgaattttctgcttcacgaatacaaatccctttttttatattcaaatacattcctgtttgtattg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0269:TDE0270|TDE0269:TDE0270:hypothetical protein:hypothetical protein:<-<-:300778..300934 157 ttgttatacaccttatttatttgtattatattttaaattaaaaaactagcggatctatgagagcgtccaactaatattctttcttaaacagatgaattttctgcttcacgaatacaaatccctttttttatattcaaatacattcctgtttgtattg Intra-Species Hit: Count: 1 Min: 1 Max: 157 Len: 157 Subject: NC_002967_TDE0269_TDE0270|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[300778,300934]|157 HSP 1 e-value: 1.0E-71 bit: 270.0 Len: 157 Query Start:1 Query End:157 Subject Strand: POSITIVE Subject Start: 1 Subject End: 157 ttgttatacaccttatttatttgtattatattttaaattaaaaaactagcggatctatgagagcgtccaactaatattctttcttaaacagatgaattttctgcttcacgaatacaaatcccnnnnnnnatattcaaatacattcctgtttgtattg ttgttatacaccttatttatttgtattatattttaaattaaaaaactagcggatctatgagagcgtccaactaatattctttcttaaacagatgaattttctgcttcacgaatacaaatccctttttttatattcaaatacattcctgtttgtattg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUUAUACACCUUAUUUAUUUGUAUUAUAUUUUAAAUUAAAAAACUAGCGGAUCUAUGAGAGCGUCCAACUAAUAUUCUUUCUUAAACAGAUGAAUUUUCUGCUUCACGAAUACAAAUCCCUUUUUUUAUAUUCAAAUACAUUCCUGUUUGUAUUG ..(((..((.((((((..((((((......(((((...))))).....))))))..))))).).))..))).............(((((((.((((........)))).(((((.(((........))).)))))..........)))))))..... (-17.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAUACAAACAGGAAUGUAUUUGAAUAUAAAAAAAGGGAUUUGUAUUCGUGAAGCAGAAAAUUCAUCUGUUUAAGAAAGAAUAUUAGUUGGACGCUCUCAUAGAUCCGCUAGUUUUUUAAUUUAAAAUAUAAUACAAAUAAAUAAGGUGUAUAACAA ..(((((.(((....))).(((((((.(((((((((((((((((.(((...(((((((.......)))))))..)))........(((.....)))...)))))))).))..)))))))))))))).....................)))))..... (-23.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 819 110 61 201 152 NC_002967:TDE0269|5end_hypothetical_protein_300687..300917_NEGATIVE 332 83 43 162 129 NC_002967:TDE1273|5end_oligopeptide/dipeptide_ABC_transporter,_peptide-binding_protein_1308624..1308854_NEGATIVE 257 84 51 35 6 NC_002967:TDE0695|5end_hypothetical_protein_731922..732152_POSITIVE 253 85 42 64 27 NC_002967:TDE0741|5end_hypothetical_protein_778158..778388_NEGATIVE 240 68 50 44 28 NC_002967:TDE2722|5end_carhohydrate_kinase,_FGGY_family_2780874..2781104_NEGATIVE 237 79 41 150 114 NC_002967:TDE1820|5end_hypothetical_protein_1854692..1854922_NEGATIVE 231 83 49 94 59 NC_002967:TDE2530|5end_radical_SAM_domain_protein_2557362..2557592_POSITIVE 225 99 57 116 78 NC_002967:TDE1989|5end_acyltransferase_family_protein_2006343..2006573_NEGATIVE 221 105 62 166 124 NC_002967:TDE2363|5end_high-affinity_branched_chain_amino_acid_ABC_transporter,_ATP-binding_protein_2398179..2398409_NEGATIVE 220 121 97 37 10 NC_002967:TDE0325|5end_hypothetical_protein_358051..358281_POSITIVE 219 67 49 20 3 NC_002967:TDE0945|5end_hypothetical_protein_967128..967358_POSITIVE 216 87 50 158 121 NC_002967:TDE1796|5end_hypothetical_protein_1835515..1835745_NEGATIVE 216 110 62 139 92 NC_002967:TDE0745|5end_glycine_reductase_complex_selenoprotein_GrdA_780287..780517_POSITIVE 213 107 61 133 80 NC_002967:TDE0599|5end_PIN_domain_protein_638577..638807_NEGATIVE 212 67 42 41 18 NC_002967:TDE0572|5end_hypothetical_protein_603494..603724_POSITIVE 211 149 105 106 63 NC_002967:TDE2108|5end_hypothetical_protein_2133495..2133725_NEGATIVE 209 87 45 231 191 NC_002967:TDE1772|5end_hypothetical_protein_1815817..1816047_NEGATIVE 206 79 39 152 109 NC_002967:TDE1832|5end_hypothetical_protein_1865921..1866151_NEGATIVE 204 107 69 111 74 NC_002967:TDE2699|5end_antigen,_putative_2742716..2742946_POSITIVE 203 148 103 210 162 NC_002967:TDE2766|5end_motility_protein_A_2820874..2821104_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 332 83 43 143 110 NC_002967:TDE1274|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1308643..1308793_NEGATIVE 302 106 61 125 81 NC_002967:TDE2327|3end_ATP-dependent_Clp_protease,_ATP-binding_subunit_ClpB_2362048..2362198_NEGATIVE 292 110 61 122 69 NC_002967:TDE0992|3end_5-formyltetrahydrofolate_cyclo-ligase_family_protein_1018321..1018471_NEGATIVE 257 84 51 35 6 NC_002967:TDE0694|3end_ABC_transporter,_ATP-binding_protein_732002..732152_POSITIVE 246 70 45 147 121 NC_002967:TDE2785|3end_hypothetical_protein_2838601..2838751_NEGATIVE 240 68 50 47 31 NC_002967:TDE2723|3end_phosphoribosylpyrophosphate_synthetase_2780871..2781021_NEGATIVE 232 68 49 135 115 NC_002967:TDE1992|3end_OmpA_family_protein_2010902..2011052_POSITIVE 225 99 57 92 54 NC_002967:TDE1990|3end_ATP-dependent_helicase,_DinG_family_2006367..2006517_NEGATIVE 222 85 49 72 39 NC_002967:TDE2050|3end_hypothetical_protein_2079707..2079857_NEGATIVE 220 121 97 50 23 NC_002967:TDE0324|3end_hypothetical_protein_358144..358294_POSITIVE 213 107 61 148 95 NC_002967:TDE0600|3end_hypothetical_protein_638562..638712_NEGATIVE 204 107 69 90 53 NC_002967:TDE2698|3end_hypothetical_protein_2742775..2742925_POSITIVE 202 126 87 92 41 NC_002967:TDE2429|3end_hypothetical_protein_2456628..2456778_NEGATIVE 200 130 87 113 69 NC_002967:TDE0043|3end_TPR_domain_protein_51651..51801_POSITIVE 199 80 43 79 39 NC_002967:TDE2480|3end_heat_shock_protein_90_2503366..2503516_NEGATIVE 198 92 51 120 76 NC_002967:TDE0875|3end_ribosomal_large_subunit_pseudouridine_synthase_B_898273..898423_POSITIVE 197 110 64 84 48 NC_002967:TDE0908|3end_ABC_transporter,_ATP-binding/permease_protein_927085..927235_POSITIVE 195 104 61 63 26 NC_002967:TDE1827|3end_hydrolase,_carbon-nitrogen_family_1859943..1860093_NEGATIVE 193 121 82 138 89 NC_002967:TDE0099|3end_adenine-specific_DNA_modification_methyltransferase_117014..117164_POSITIVE 192 128 90 54 26 NC_002967:TDE2522|3end_ABC_transporter,_ATP-binding_protein_2550004..2550154_POSITIVE