Origin IGS: gagattatggtttgaaaaggacccgatatgtaatcgggtctttttttttgattaaatctttaataaaaataatcacaacagggtagaattataaatttataaaataaagtactttacaaaataaagtaggtatgctattatcatataggaatctaaggaggttcata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tatgaacctccttagattcctatatgataatagcatacctactttattttgtaaagtactttattttataaatttataattctaccctgttgtgattatttttattaaagatttaatcaaaaaaaaagacccgattacatatcgggtccttttcaaaccataatctc Mask Tandem Repeat Region ================================================ gagattatggtttgaaaaggacccgatatgtaatcgggtctttttttttgattaaatctttaataaaaataatcacaacagggtagaattataaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnggtatgctattatcatataggaatctaaggaggttcata Find is-nt database================================================ Query_seq: TDE1483:TDE1484|TDE1483:TDE1484:hypothetical protein:hypothetical protein:->->:1529128..1529294 167 gagattatggtttgaaaaggacccgatatgtaatcgggtctttttttttgattaaatctttaataaaaataatcacaacagggtagaattataaatttataaaataaagtactttacaaaataaagtaggtatgctattatcatataggaatctaaggaggttcata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1483:TDE1484|TDE1483:TDE1484:hypothetical protein:hypothetical protein:->->:1529128..1529294 167 gagattatggtttgaaaaggacccgatatgtaatcgggtctttttttttgattaaatctttaataaaaataatcacaacagggtagaattataaatttataaaataaagtactttacaaaataaagtaggtatgctattatcatataggaatctaaggaggttcata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1483:TDE1484|TDE1483:TDE1484:hypothetical protein:hypothetical protein:->->:1529128..1529294 167 gagattatggtttgaaaaggacccgatatgtaatcgggtctttttttttgattaaatctttaataaaaataatcacaacagggtagaattataaatttataaaataaagtactttacaaaataaagtaggtatgctattatcatataggaatctaaggaggttcata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gagattatggtttgaaaaggacccgatatgtaatcgggtctttttttttgattaaatctttaataaaaataatcacaacagggtagaattataaatttataaaataaagtactttacaaaataaagtaggtatgctattatcatataggaatctaaggaggttcata Predict ORF larger than 30AA ================================================ gagattatggtttgaaaaggacccgatatgtaatcgggtctttttttttgattaaatctttaataaaaataatcacaacagggtagaattataaatttataaaataaagtactttacaaaataaagtaggtatgctattatcatataggaatctaaggaggttcata 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: 112 End: 141 ...............................................................................................................CTTTACAAAATAAAGTAGGTATGCTATTAT.......................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gagattatggtttgaaaaggacccgatatgtaatcgggtctttttttttgattaaatctttaataaaaataatcacaacagggtagaattataaatttataaaataaagtactttacaaaataaagtaggtatgctattatcatataggaatctaaggaggttcata Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 77 HP_score: -7.7 Tail_Score: -4.08945 Start: 19 End: 41 Full_Region: tttaatcaaaaaaaa agacccgat tacat atcgggtcc ttttcaaaccataat ..................agacccgattacatatcgggtcc.............................................................................................................................. TransTerm Strand: - Conf: 87 HP_score: -11.2 Tail_Score: -3.05046 Start: 20 End: 40 Full_Region: ttaatcaaaaaaaaa gacccgat tacat atcgggtc cttttcaaaccataa ...................gacccgattacatatcgggtc............................................................................................................................... Find igs database================================================ Query_seq: TDE1483:TDE1484|TDE1483:TDE1484:hypothetical protein:hypothetical protein:->->:1529128..1529294 167 gagattatggtttgaaaaggacccgatatgtaatcgggtctttttttttgattaaatctttaataaaaataatcacaacagggtagaattataaatttataaaataaagtactttacaaaataaagtaggtatgctattatcatataggaatctaaggaggttcata Intra-Species Hit: Count: 1 Min: 1 Max: 167 Len: 167 Subject: NC_002967_TDE1483_TDE1484|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1529128,1529294]|167 HSP 1 e-value: 6.0E-74 bit: 278.0 Len: 167 Query Start:1 Query End:167 Subject Strand: POSITIVE Subject Start: 1 Subject End: 167 gagattatggtttgaaaaggacccgatatgtaatcgggtcnnnnnnnnngattaaatctttaataaaaataatcacaacagggtagaattataaatttataaaataaagtactttacaaaataaagtaggtatgctattatcatataggaatctaaggaggttcata gagattatggtttgaaaaggacccgatatgtaatcgggtctttttttttgattaaatctttaataaaaataatcacaacagggtagaattataaatttataaaataaagtactttacaaaataaagtaggtatgctattatcatataggaatctaaggaggttcata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGAUUAUGGUUUGAAAAGGACCCGAUAUGUAAUCGGGUCUUUUUUUUUGAUUAAAUCUUUAAUAAAAAUAAUCACAACAGGGUAGAAUUAUAAAUUUAUAAAAUAAAGUACUUUACAAAAUAAAGUAGGUAUGCUAUUAUCAUAUAGGAAUCUAAGGAGGUUCAUA ((((((.(((((.((((((((((((((.....))))))))))))))...))))))))))).....................(((((..(((((....))))).......(((((((.....)))))))......))))).........((((((....))))))... (-35.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUGAACCUCCUUAGAUUCCUAUAUGAUAAUAGCAUACCUACUUUAUUUUGUAAAGUACUUUAUUUUAUAAAUUUAUAAUUCUACCCUGUUGUGAUUAUUUUUAUUAAAGAUUUAAUCAAAAAAAAAGACCCGAUUACAUAUCGGGUCCUUUUCAAACCAUAAUCUC ((((......(((.(((......((.(((((((..............(((((((((((...)))))))))))..............))))))).)).......))).)))............((((.((((((((.....)))))))).)))).....))))..... (-27.31) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 270 50 10 46 5 NC_002967:TDE1411|5end_hypothetical_protein_1453402..1453632_NEGATIVE 246 47 8 221 182 NC_002967:TDE2260|5end_hypothetical_protein_2297338..2297568_POSITIVE 240 37 7 215 185 NC_002967:TDE2722|5end_carhohydrate_kinase,_FGGY_family_2780874..2781104_NEGATIVE 238 36 8 68 34 NC_002967:TDE2152|5end_hypothetical_protein_2189103..2189333_NEGATIVE 225 65 21 228 182 NC_002967:TDE2256|5end_hypothetical_protein_2293387..2293617_NEGATIVE 223 50 3 62 20 NC_002967:TDE0198|5end_hypothetical_protein_233155..233385_POSITIVE 221 39 2 151 105 NC_002967:TDE1760|5end_HD_domain_protein_1809868..1810098_NEGATIVE 216 60 19 99 51 NC_002967:TDE0743|5end_thioredoxin_reductase_778718..778948_POSITIVE 215 43 9 215 185 NC_002967:TDE0096|5end_NADH_oxidase_112723..112953_POSITIVE 211 50 8 106 67 NC_002967:TDE1601|5end_transcriptional_regulator,_TetR_family_1653036..1653266_NEGATIVE 209 50 9 171 128 NC_002967:TDE2346|5end_elongation_factor_Ts_2383429..2383659_NEGATIVE 207 48 7 49 6 NC_002967:TDE1740|5end_hypothetical_protein_1792785..1793015_NEGATIVE 204 43 7 157 114 NC_002967:TDE0671|5end_PIN_domain_protein_710621..710851_POSITIVE 200 60 18 204 163 NC_002967:TDE1521|5end_fumarate_hydratase_1567211..1567441_POSITIVE 200 44 23 170 146 NC_002967:TDE1004|5end_flagellar_filament_core_protein_1030136..1030366_NEGATIVE 199 59 18 77 44 NC_002967:TDE1547|5end_ribonuclease_HII_1591124..1591354_POSITIVE 199 50 10 77 32 NC_002967:TDE0975|5end_hypothetical_protein_998921..999151_POSITIVE 199 155 121 38 9 NC_002967:TDE0720|5end_bacteriocin_ABC_transporter,_bacteriocin-binding_protein,_putative_755612..755842_POSITIVE 199 160 116 46 4 NC_002967:TDE0461|5end_hypothetical_protein_515863..516093_POSITIVE 199 41 18 225 201 NC_002967:TDE0082|5end_transcriptional_regulator,_MerR_family_94251..94481_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 310 45 9 76 33 NC_002967:TDE1483|3end_hypothetical_protein_1529067..1529217_POSITIVE 261 60 13 53 6 NC_002967:TDE0095|3end_hypothetical_protein_112622..112772_POSITIVE 255 50 8 118 64 NC_002967:TDE2097|3end_hypothetical_protein_2124478..2124628_NEGATIVE 246 49 12 151 111 NC_002967:TDE0996|3end_hypothetical_protein_1023998..1024148_POSITIVE 238 36 8 62 28 NC_002967:TDE2153|3end_hypothetical_protein_2189109..2189259_NEGATIVE 228 41 16 30 7 NC_002967:TDE2038|3end_UVR_domain_protein_2067704..2067854_NEGATIVE 228 49 1 128 84 NC_002967:TDE1239|3end_hypothetical_protein_1271217..1271367_NEGATIVE 225 65 21 112 66 NC_002967:TDE2257|3end_5'-nucleotidase_family_protein_2293503..2293653_NEGATIVE 223 50 3 52 10 NC_002967:TDE0197|3end_PIN_domain_protein_233225..233375_POSITIVE 221 39 2 139 93 NC_002967:TDE1761|3end_hypothetical_protein_1809880..1810030_NEGATIVE 214 60 11 117 70 NC_002967:TDE1063|3end_methionyl-tRNA_synthetase_1092968..1093118_POSITIVE 210 47 9 41 7 NC_002967:TDE1252|3end_lipoprotein,_putative_1287094..1287244_POSITIVE 209 50 9 97 54 NC_002967:TDE2347|3end_30S_ribosomal_protein_S2_2383503..2383653_NEGATIVE 203 48 3 92 42 NC_002967:TDE0012|3end_carbon_starvation_protein_CstA,_putative_17702..17852_POSITIVE 201 50 1 148 84 NC_002967:TDE0799|3end_glycerophosphoryl_diester_phosphodiesterase,_putative_823468..823618_POSITIVE 199 59 18 77 44 NC_002967:TDE1546|3end_hypothetical_protein_1591204..1591354_POSITIVE 199 155 121 41 12 NC_002967:TDE0719|3end_bacteriocin_ABC_transporter,_ATP-binding/permease_protein,_putative_755695..755845_POSITIVE 197 61 23 49 1 NC_002967:TDE2507|3end_hypothetical_protein_2531643..2531793_NEGATIVE 196 50 11 150 115 NC_002967:TDE2320|3end_RNA_polymerase_sigma-24_factor,_putative_2356310..2356460_NEGATIVE 195 38 1 63 19 NC_002967:TDE1623|3end_hypothetical_protein_1671018..1671168_NEGATIVE