Origin IGS: actaatctcctaaaaaacagcttaaaattttaagcattataatgtttgttttccaaagtatacacgatgatcttaataaaagcaaggggagaaaaaagtttgttactacggatttttaggtttaatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aattaaacctaaaaatccgtagtaacaaacttttttctccccttgcttttattaagatcatcgtgtatactttggaaaacaaacattataatgcttaaaattttaagctgttttttaggagattagt Mask Tandem Repeat Region ================================================ actaatctcctaaaaaacagcttaaaattttaagcattataatgtttgttttccaaagtatacacgatgatcttaataaaagcaaggggagaaaaaagtttgttactacggatttttaggtttaatt Find is-nt database================================================ Query_seq: TDE1629:TDE1630|TDE1629:TDE1630:dihydrolipoamide dehydrogenase:hypothetical protein:<-<-:1678605..1678731 127 actaatctcctaaaaaacagcttaaaattttaagcattataatgtttgttttccaaagtatacacgatgatcttaataaaagcaaggggagaaaaaagtttgttactacggatttttaggtttaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1629:TDE1630|TDE1629:TDE1630:dihydrolipoamide dehydrogenase:hypothetical protein:<-<-:1678605..1678731 127 actaatctcctaaaaaacagcttaaaattttaagcattataatgtttgttttccaaagtatacacgatgatcttaataaaagcaaggggagaaaaaagtttgttactacggatttttaggtttaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1629:TDE1630|TDE1629:TDE1630:dihydrolipoamide dehydrogenase:hypothetical protein:<-<-:1678605..1678731 127 actaatctcctaaaaaacagcttaaaattttaagcattataatgtttgttttccaaagtatacacgatgatcttaataaaagcaaggggagaaaaaagtttgttactacggatttttaggtttaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actaatctcctaaaaaacagcttaaaattttaagcattataatgtttgttttccaaagtatacacgatgatcttaataaaagcaaggggagaaaaaagtttgttactacggatttttaggtttaatt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 27 End: 116 .......................... M L S I I M F V F Q S I H D D L N K S K G R K K F V T T D F ........... actaatctcctaaaaaacagcttaaaattttaagcattataatgtttgttttccaaagtatacacgatgatcttaataaaagcaaggggagaaaaaagtttgttactacggatttttaggtttaatt 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: 81 Start: 27 End: 56 ..........................TTGGAAAACAAACATTATAATGCTTAAAAT....................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ actaatctcctaaaaaacagcttaaaattttaagcattataatgtttgttttccaaagtatacacgatgatcttaataaaagcaaggggagaaaaaagtttgttactacggatttttaggtttaatt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 70 HP_score: -6.2 Tail_Score: -4.13963 Start: 20 End: 35 Full_Region: aacaaacattataat gcttaa aatt ttaagc tgttttttaggagat ...................gcttaaaattttaagc............................................................................................ Find igs database================================================ Query_seq: TDE1629:TDE1630|TDE1629:TDE1630:dihydrolipoamide dehydrogenase:hypothetical protein:<-<-:1678605..1678731 127 actaatctcctaaaaaacagcttaaaattttaagcattataatgtttgttttccaaagtatacacgatgatcttaataaaagcaaggggagaaaaaagtttgttactacggatttttaggtttaatt Intra-Species Hit: Count: 1 Min: 1 Max: 127 Len: 127 Subject: NC_002967_TDE1629_TDE1630|dihydrolipoamide dehydrogenase:hypothetical protein|NEGATIVE:NEGATIVE|[1678605,1678731]|127 HSP 1 e-value: 2.0E-66 bit: 252.0 Len: 127 Query Start:1 Query End:127 Subject Strand: POSITIVE Subject Start: 1 Subject End: 127 actaatctcctaaaaaacagcttaaaattttaagcattataatgtttgttttccaaagtatacacgatgatcttaataaaagcaaggggagaaaaaagtttgttactacggatttttaggtttaatt actaatctcctaaaaaacagcttaaaattttaagcattataatgtttgttttccaaagtatacacgatgatcttaataaaagcaaggggagaaaaaagtttgttactacggatttttaggtttaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUAAUCUCCUAAAAAACAGCUUAAAAUUUUAAGCAUUAUAAUGUUUGUUUUCCAAAGUAUACACGAUGAUCUUAAUAAAAGCAAGGGGAGAAAAAAGUUUGUUACUACGGAUUUUUAGGUUUAAUU .....((((((........((((((....))))))..........(((((((...(((.............)))....))))))).)))))).((((((((((....)))))))))).......... (-21.22) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUAAACCUAAAAAUCCGUAGUAACAAACUUUUUUCUCCCCUUGCUUUUAUUAAGAUCAUCGUGUAUACUUUGGAAAACAAACAUUAUAAUGCUUAAAAUUUUAAGCUGUUUUUUAGGAGAUUAGU .......((((((((((((.(((((((........(((................)))......))).)))).))))................((((((....))))))...))))))))........ (-18.43) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 797 110 61 201 152 NC_002967:TDE1629|5end_dihydrolipoamide_dehydrogenase_1678514..1678744_NEGATIVE 244 89 41 181 133 NC_002967:TDE0680|5end_protein-export_membrane_protein_SecF_718854..719084_NEGATIVE 241 98 63 194 159 NC_002967:TDE0351|5end_L-lactate_dehydrogenase_395998..396228_NEGATIVE 235 59 21 112 75 NC_002967:TDE0867|5end_hypothetical_protein_888542..888772_POSITIVE 231 112 77 46 11 NC_002967:TDE1044|5end_hypothetical_protein_1072075..1072305_POSITIVE 228 51 14 231 196 NC_002967:TDE2011|5end_hypothetical_protein_2031930..2032160_POSITIVE 221 102 72 78 39 NC_002967:TDE1091|5end_hypothetical_protein_1123775..1124005_NEGATIVE 220 98 54 50 10 NC_002967:TDE1313|5end_signal_peptidase_I_1350650..1350880_POSITIVE 214 111 71 159 117 NC_002967:TDE1904|5end_hypothetical_protein_1923613..1923843_NEGATIVE 211 89 41 228 158 NC_002967:TDE0949|5end_enolase_972010..972240_POSITIVE 210 89 41 88 38 NC_002967:TDE0717|5end_hypothetical_protein_751779..752009_POSITIVE 209 94 51 62 5 NC_002967:TDE2133|5end_cobalt_transport_protein,_putative_2164323..2164553_NEGATIVE 209 105 64 127 97 NC_002967:TDE1592|5end_ABC_transporter,_ATP-binding_protein_1639491..1639721_POSITIVE 206 100 51 168 120 NC_002967:TDE0464|5end_NifU_domain_protein_518175..518405_NEGATIVE 205 87 50 113 76 NC_002967:TDE0585|5end_hypothetical_protein_625024..625254_NEGATIVE 204 107 82 178 156 NC_002967:TDE1267|5end_phosphoribosylamine--glycine_ligase_1302940..1303170_NEGATIVE 202 112 79 51 18 NC_002967:TDE0076|5end_aldolase,_DeoC/FbaB_family_87386..87616_NEGATIVE 199 90 49 54 7 NC_002967:TDE1392|5end_hypothetical_protein_1432002..1432232_POSITIVE 199 120 84 168 129 NC_002967:TDE1059|5end_hypothetical_protein_1086605..1086835_NEGATIVE 196 89 41 80 28 NC_002967:TDE0021|5end_CDP-alcohol_phosphatidyltransferase_family_protein_26814..27044_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 242 55 14 140 99 NC_002967:TDE2010|3end_hypothetical_protein_2031913..2032063_POSITIVE 235 59 21 119 82 NC_002967:TDE0866|3end_hypothetical_protein_888629..888779_POSITIVE 231 112 77 49 14 NC_002967:TDE1043|3end_hypothetical_protein_1072158..1072308_POSITIVE 221 102 72 47 8 NC_002967:TDE1092|3end_hypothetical_protein_1123806..1123956_NEGATIVE 214 111 71 50 8 NC_002967:TDE1905|3end_hypothetical_protein_1923722..1923872_NEGATIVE 210 99 55 77 30 NC_002967:TDE2230|3end_hypothetical_protein_2269453..2269603_POSITIVE 209 105 64 72 42 NC_002967:TDE1591|3end_inorganic_polyphosphate/ATP-NAD_kinase,_putative_1639516..1639666_POSITIVE 206 100 51 75 27 NC_002967:TDE0465|3end_PIN_domain_protein_518268..518418_NEGATIVE 204 107 82 98 76 NC_002967:TDE1268|3end_type_II_restriction_endonuclease_TdeI_1303020..1303170_NEGATIVE 201 105 63 146 108 NC_002967:TDE0717|3end_hypothetical_protein_752380..752530_POSITIVE 199 90 49 61 14 NC_002967:TDE1391|3end_NQR2/RnfD/RnfE_family_protein_1432089..1432239_POSITIVE 196 89 41 67 15 NC_002967:TDE0020|3end_glycyl-tRNA_synthetase_26881..27031_POSITIVE 195 100 73 92 62 NC_002967:TDE1249|3end_hypothetical_protein_1284540..1284690_POSITIVE 194 91 55 44 8 NC_002967:TDE0959|3end_hypothetical_protein_982365..982515_POSITIVE 192 102 78 76 53 NC_002967:TDE2528|3end_hypothetical_protein_2556220..2556370_NEGATIVE 191 37 1 61 22 NC_002967:TDE1041|3end_polyribonucleotide_nucleotidyltransferase_1070500..1070650_POSITIVE 190 120 86 95 58 NC_002967:TDE0569|3end_hypothetical_protein_600162..600312_POSITIVE 188 43 2 128 76 NC_002967:TDE2065|3end_FeoA_family_protein_2091516..2091666_NEGATIVE 186 100 53 42 1 NC_002967:TDE1400|3end_NAD(+)_synthetase_1442434..1442584_POSITIVE 185 59 18 149 104 NC_002967:TDE0681|3end_protein_export_protein_SecD_718856..719006_NEGATIVE