Origin IGS: cttataatctcctcgtaattttatactatttcgatttaagttggatgtgttgccattacatttttctcacctctacaaattctaatttgttttactcgatgtttgtaata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tattacaaacatcgagtaaaacaaattagaatttgtagaggtgagaaaaatgtaatggcaacacatccaacttaaatcgaaatagtataaaattacgaggagattataag Mask Tandem Repeat Region ================================================ cttataatctcctcgtaattttatactatttcgatttaagttggatgtgttgccattacatttttctcacctctacaaattctaatttgttttactcgatgtttgtaata Find is-nt database================================================ Query_seq: TDE2171:TDE2172|TDE2171:TDE2172:hypothetical protein:hypothetical protein:<-<-:2202632..2202741 110 cttataatctcctcgtaattttatactatttcgatttaagttggatgtgttgccattacatttttctcacctctacaaattctaatttgttttactcgatgtttgtaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2171:TDE2172|TDE2171:TDE2172:hypothetical protein:hypothetical protein:<-<-:2202632..2202741 110 cttataatctcctcgtaattttatactatttcgatttaagttggatgtgttgccattacatttttctcacctctacaaattctaatttgttttactcgatgtttgtaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2171:TDE2172|TDE2171:TDE2172:hypothetical protein:hypothetical protein:<-<-:2202632..2202741 110 cttataatctcctcgtaattttatactatttcgatttaagttggatgtgttgccattacatttttctcacctctacaaattctaatttgttttactcgatgtttgtaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttataatctcctcgtaattttatactatttcgatttaagttggatgtgttgccattacatttttctcacctctacaaattctaatttgttttactcgatgtttgtaata Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 18 End: 110 ................. M L Y Y F D L S W M C C H Y I F L T S T N S N L F Y S M F V I cttataatctcctcgtaattttatactatttcgatttaagttggatgtgttgccattacatttttctcacctctacaaattctaatttgttttactcgatgtttgtaata 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================================================ cttataatctcctcgtaattttatactatttcgatttaagttggatgtgttgccattacatttttctcacctctacaaattctaatttgttttactcgatgtttgtaata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2171:TDE2172|TDE2171:TDE2172:hypothetical protein:hypothetical protein:<-<-:2202632..2202741 110 cttataatctcctcgtaattttatactatttcgatttaagttggatgtgttgccattacatttttctcacctctacaaattctaatttgttttactcgatgtttgtaata Intra-Species Hit: Count: 1 Min: 1 Max: 110 Len: 110 Subject: NC_002967_TDE2171_TDE2172|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[2202632,2202741]|110 HSP 1 e-value: 3.0E-56 bit: 218.0 Len: 110 Query Start:1 Query End:110 Subject Strand: POSITIVE Subject Start: 1 Subject End: 110 cttataatctcctcgtaattttatactatttcgatttaagttggatgtgttgccattacatttttctcacctctacaaattctaatttgttttactcgatgtttgtaata cttataatctcctcgtaattttatactatttcgatttaagttggatgtgttgccattacatttttctcacctctacaaattctaatttgttttactcgatgtttgtaata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUAUAAUCUCCUCGUAAUUUUAUACUAUUUCGAUUUAAGUUGGAUGUGUUGCCAUUACAUUUUUCUCACCUCUACAAAUUCUAAUUUGUUUUACUCGAUGUUUGUAAUA .((((((.(((...(((((...((((...((((((....)))))).))))....)))))...............((((((....)))))).......)).).)))))).. (-12.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUACAAACAUCGAGUAAAACAAAUUAGAAUUUGUAGAGGUGAGAAAAAUGUAAUGGCAACACAUCCAACUUAAAUCGAAAUAGUAUAAAAUUACGAGGAGAUUAUAAG (((((((....(((..(...((((((....))))))..)..)))......))))))).............((((((((......(((......))).....)))).)))) (-12.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 805 80 31 171 122 NC_002967:TDE2171|5end_hypothetical_protein_2202541..2202771_NEGATIVE 272 45 2 138 91 NC_002967:TDE0748|5end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_784288..784518_NEGATIVE 254 53 11 147 112 NC_002967:TDE2158|5end_ABC_transporter,_ATP-binding_protein_2191664..2191894_POSITIVE 246 104 69 132 96 NC_002967:TDE0923|5end_ABC_transporter,_ATP-binding/permease_protein_945731..945961_NEGATIVE 239 50 2 146 92 NC_002967:TDE0526|5end_hypothetical_protein_571441..571671_POSITIVE 229 87 41 159 106 NC_002967:TDE2198|5end_pyruvate-ferredoxin_oxidoreductase_2236507..2236737_NEGATIVE 227 77 31 115 66 NC_002967:TDE2245|5end_DNA_topoisomerase_IV_subunit_B_2284240..2284470_POSITIVE 226 90 41 99 54 NC_002967:TDE0578|5end_hypothetical_protein_609493..609723_POSITIVE 214 90 45 121 74 NC_002967:TDE1306|5end_hypothetical_protein_1340874..1341104_NEGATIVE 213 65 25 165 123 NC_002967:TDE1555|5end_hypothetical_protein_1598018..1598248_POSITIVE 213 53 11 55 16 NC_002967:TDE1229|5end_hypothetical_protein_1262413..1262643_POSITIVE 209 69 26 104 55 NC_002967:TDE0556|5end_hypothetical_protein_592092..592322_NEGATIVE 204 73 51 127 107 NC_002967:TDE2097|5end_hypothetical_protein_2124741..2124971_NEGATIVE 204 69 24 90 38 NC_002967:TDE1456|5end_GGDEF_domain_protein_1504739..1504969_NEGATIVE 202 69 23 98 60 NC_002967:TDE0596|5end_hypothetical_protein_636010..636240_NEGATIVE 202 45 1 131 87 NC_002967:TDE0042|5end_phosphate_acetyltransferase_48676..48906_POSITIVE 200 54 38 203 187 NC_002967:TDE2587|5end_endonuclease/exonuclease/phosphatase_family_protein_2622191..2622421_POSITIVE 200 61 32 203 175 NC_002967:TDE2065|5end_FeoA_family_protein_2091779..2092009_NEGATIVE 199 56 11 131 85 NC_002967:TDE2769|5end_flagellar_hook_assembly_protein_2823032..2823262_NEGATIVE 198 44 1 126 87 NC_002967:TDE2420|5end_DNA-directed_RNA_polymerase_beta'_subunit_2449234..2449464_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 254 53 11 135 100 NC_002967:TDE2157|3end_ABC_transporter,_permease_protein,_putative_2191732..2191882_POSITIVE 246 104 69 112 76 NC_002967:TDE0924|3end_ABC_transporter,_ATP-binding/permease_protein_945751..945901_NEGATIVE 227 77 31 115 66 NC_002967:TDE2244|3end_hypothetical_protein_2284320..2284470_POSITIVE 221 67 21 59 12 NC_002967:TDE0514|3end_hypothetical_protein_562420..562570_NEGATIVE 214 90 48 72 27 NC_002967:TDE0343|3end_hydrolase,_alpha/beta_fold_family_384247..384397_NEGATIVE 213 53 11 58 19 NC_002967:TDE1228|3end_pentapeptide_repeat_family_protein_1262496..1262646_POSITIVE 212 63 42 96 76 NC_002967:TDE0219|3end_hypothetical_protein_253356..253506_NEGATIVE 209 69 26 50 1 NC_002967:TDE0557|3end_hypothetical_protein_592146..592296_NEGATIVE 204 69 24 90 38 NC_002967:TDE1457|3end_hypothetical_protein_1504739..1504889_NEGATIVE 202 69 23 89 51 NC_002967:TDE0597|3end_hypothetical_protein_636019..636169_NEGATIVE 199 56 11 119 73 NC_002967:TDE2770|3end_flagellar_hook-length_control_protein_FliK_2823044..2823194_NEGATIVE 198 44 1 101 62 NC_002967:TDE2421|3end_DNA-directed_RNA_polymerase_beta_subunit_2449259..2449409_NEGATIVE 198 44 8 115 81 NC_002967:TDE0429|3end_hypothetical_protein_485205..485355_NEGATIVE 197 58 11 63 26 NC_002967:TDE2129|3end_hypothetical_protein_2161635..2161785_POSITIVE 196 48 1 104 60 NC_002967:TDE0289|3end_hypothetical_protein_320071..320221_NEGATIVE 195 70 26 44 2 NC_002967:TDE1145|3end_hypothetical_protein_1182868..1183018_NEGATIVE 195 52 11 143 96 NC_002967:TDE1096|3end_hydroxymethylbutenyl_pyrophosphate_reductase_1131938..1132088_POSITIVE 194 75 31 109 63 NC_002967:TDE0986|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1014121..1014271_POSITIVE 193 101 62 72 41 NC_002967:TDE2436|3end_hypothetical_protein_2467446..2467596_POSITIVE 193 84 51 125 87 NC_002967:TDE1208|3end_DNA_topoisomerase_I_1242432..1242582_POSITIVE