Origin IGS: cctctttaaacttattgagcgcggttgatgagattaaccgtttggtggaaagtacaatcgtaaggaaaacctcaaaaagctgaagttttcgaggttccctttag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctaaagggaacctcgaaaacttcagctttttgaggttttccttacgattgtactttccaccaaacggttaatctcatcaaccgcgctcaataagtttaaagagg Mask Tandem Repeat Region ================================================ cctctttaaacttattgagcgcggttgatgagattaaccgtttggtggaaagtacaatcgtaaggaaaacctcaaaaagctgaagttttcgaggttccctttag Find is-nt database================================================ Query_seq: TDE0355:TDE0356|TDE0355:TDE0356:hypothetical protein:hypothetical protein:-><-:399718..399821 104 cctctttaaacttattgagcgcggttgatgagattaaccgtttggtggaaagtacaatcgtaaggaaaacctcaaaaagctgaagttttcgaggttccctttag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0355:TDE0356|TDE0355:TDE0356:hypothetical protein:hypothetical protein:-><-:399718..399821 104 cctctttaaacttattgagcgcggttgatgagattaaccgtttggtggaaagtacaatcgtaaggaaaacctcaaaaagctgaagttttcgaggttccctttag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0355:TDE0356|TDE0355:TDE0356:hypothetical protein:hypothetical protein:-><-:399718..399821 104 cctctttaaacttattgagcgcggttgatgagattaaccgtttggtggaaagtacaatcgtaaggaaaacctcaaaaagctgaagttttcgaggttccctttag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cctctttaaacttattgagcgcggttgatgagattaaccgtttggtggaaagtacaatcgtaaggaaaacctcaaaaagctgaagttttcgaggttccctttag Predict ORF larger than 30AA ================================================ cctctttaaacttattgagcgcggttgatgagattaaccgtttggtggaaagtacaatcgtaaggaaaacctcaaaaagctgaagttttcgaggttccctttag 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================================================ cctctttaaacttattgagcgcggttgatgagattaaccgtttggtggaaagtacaatcgtaaggaaaacctcaaaaagctgaagttttcgaggttccctttag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0355:TDE0356|TDE0355:TDE0356:hypothetical protein:hypothetical protein:-><-:399718..399821 104 cctctttaaacttattgagcgcggttgatgagattaaccgtttggtggaaagtacaatcgtaaggaaaacctcaaaaagctgaagttttcgaggttccctttag Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: NC_002967_TDE0355_TDE0356|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[399718,399821]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 cctctttaaacttattgagcgcggttgatgagattaaccgtttggtggaaagtacaatcgtaaggaaaacctcaaaaagctgaagttttcgaggttccctttag cctctttaaacttattgagcgcggttgatgagattaaccgtttggtggaaagtacaatcgtaaggaaaacctcaaaaagctgaagttttcgaggttccctttag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUCUUUAAACUUAUUGAGCGCGGUUGAUGAGAUUAACCGUUUGGUGGAAAGUACAAUCGUAAGGAAAACCUCAAAAAGCUGAAGUUUUCGAGGUUCCCUUUAG ...........((((..(..(((((((((...))))))))))..))))............(((((..((((((..(((((....))))).))))))..))))). (-23.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUAAAGGGAACCUCGAAAACUUCAGCUUUUUGAGGUUUUCCUUACGAUUGUACUUUCCACCAAACGGUUAAUCUCAUCAACCGCGCUCAAUAAGUUUAAAGAGG ...(((((((((((((((((....).))))))))).)))))))....(((.((((.........(((((.........)))))........)))).)))..... (-21.73) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 468 98 56 209 168 NC_002967:TDE0332|5end_transcriptional_regulator,_TetR_family_370940..371170_POSITIVE 401 100 63 38 1 NC_002967:TDE2027|5end_hypothetical_protein_2052649..2052879_POSITIVE 366 97 51 62 17 NC_002967:TDE1853|5end_hypothetical_protein_1882082..1882312_NEGATIVE 356 98 64 201 167 NC_002967:TDE0943|5end_hypothetical_protein_965983..966213_POSITIVE 342 100 63 149 110 NC_002967:TDE0346|5end_protease_PrtB_387897..388127_NEGATIVE 302 99 51 54 5 NC_002967:TDE0331|5end_hypothetical_protein_370943..371173_NEGATIVE 281 70 21 61 6 NC_002967:TDE0156|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_183571..183801_NEGATIVE 279 100 51 177 125 NC_002967:TDE0855|5end_DNA-binding_response_regulator_876536..876766_POSITIVE 278 100 68 160 127 NC_002967:TDE2062|5end_hypothetical_protein_2088344..2088574_NEGATIVE 266 60 15 174 129 NC_002967:TDE1287|5end_transcription-repair_coupling_factor_1322738..1322968_POSITIVE 260 49 1 154 98 NC_002967:TDE1876|5end_glycosyl_transferase,_WecB/TagA/CpsF_family_1897679..1897909_NEGATIVE 255 100 63 152 116 NC_002967:TDE2256|5end_hypothetical_protein_2293387..2293617_NEGATIVE 254 46 21 58 33 NC_002967:TDE2266|5end_reverse_transcriptase_family_protein_2304028..2304258_NEGATIVE 253 96 55 83 48 NC_002967:TDE2413|5end_hypothetical_protein_2440988..2441218_NEGATIVE 251 48 1 60 10 NC_002967:TDE2456|5end_hypothetical_protein_2484573..2484803_NEGATIVE 249 60 11 159 101 NC_002967:TDE0791|5end_DNA-directed_RNA_polymerase_alpha_subunit_817342..817572_POSITIVE 248 65 21 138 70 NC_002967:TDE2311|5end_hypothetical_protein_2348238..2348468_POSITIVE 246 90 45 64 14 NC_002967:TDE1225|5end_zinc_ABC_transporter,_ATP-binding_protein_1259518..1259748_NEGATIVE 246 65 22 187 128 NC_002967:TDE0491|5end_hypothetical_protein_546716..546946_POSITIVE 246 94 58 215 177 NC_002967:TDE0171|5end_nuclease_SbcCD,_C_subunit,_putative_199965..200195_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 472 100 56 67 23 NC_002967:TDE0186|3end_hypothetical_protein_222373..222523_NEGATIVE 430 96 61 81 44 NC_002967:TDE1993|3end_aspartate_ammonia-lyase,_putative_2010917..2011067_NEGATIVE 359 100 62 84 45 NC_002967:TDE1263|3end_hypothetical_protein_1298136..1298286_POSITIVE 356 98 64 77 43 NC_002967:TDE0942|3end_long-chain-fatty-acid--CoA_ligase,_putative_965939..966089_POSITIVE 329 96 59 81 43 NC_002967:TDE0525|3end_hypothetical_protein_571163..571313_POSITIVE 296 48 9 83 40 NC_002967:TDE2621|3end_hypothetical_protein_2662197..2662347_POSITIVE 289 100 63 90 52 NC_002967:TDE1264|3end_hypothetical_protein_1298152..1298302_NEGATIVE 279 100 51 122 70 NC_002967:TDE0854|3end_regulatory_protein_RecX_876561..876711_POSITIVE 278 100 68 74 41 NC_002967:TDE2063|3end_ferrous_iron_transport_protein_B_2088430..2088580_NEGATIVE 271 100 64 87 49 NC_002967:TDE2029|3end_hydrolase,_TatD_family_2057148..2057298_NEGATIVE 267 43 1 149 106 NC_002967:TDE2192|3end_threonine_synthase_2229259..2229409_POSITIVE 263 53 11 110 57 NC_002967:TDE2773|3end_hypothetical_protein_2825823..2825973_NEGATIVE 263 60 17 71 22 NC_002967:TDE0536|3end_hypothetical_protein_578064..578214_NEGATIVE 254 46 21 104 79 NC_002967:TDE2267|3end_HRDC_domain_protein_2303982..2304132_NEGATIVE 254 97 62 81 47 NC_002967:TDE0151|3end_integral_membrane_protein,_YeeE/YedE_family_171845..171995_NEGATIVE 253 96 55 50 15 NC_002967:TDE2414|3end_hypothetical_protein_2441021..2441171_NEGATIVE 250 100 70 36 5 NC_002967:TDE2257|3end_5'-nucleotidase_family_protein_2293503..2293653_NEGATIVE 250 59 11 64 16 NC_002967:TDE1463|3end_hypothetical_protein_1512206..1512356_NEGATIVE 249 56 11 51 8 NC_002967:TDE0919|3end_hypothetical_protein_939125..939275_POSITIVE 249 60 11 148 90 NC_002967:TDE0790|3end_30S_ribosomal_protein_S11_817411..817561_POSITIVE