Origin IGS: actttaaactcttgattaaacttgttttctacttgaaaaaatgagaataaaatgctagtatcttaagagctgtgatagttgtttagctttacagtataatgaaataacttaaattggagggttattaag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cttaataaccctccaatttaagttatttcattatactgtaaagctaaacaactatcacagctcttaagatactagcattttattctcattttttcaagtagaaaacaagtttaatcaagagtttaaagt Mask Tandem Repeat Region ================================================ actttaaactcttgattaaacttgttttctacttgaaaaaatgagaataaaatgctagtatcttaagagctgtgatagttgtttagctttacagtataatgaaataacttaaattggagggttattaag Find is-nt database================================================ Query_seq: TDE1236:TDE1237|TDE1236:TDE1237:triosephosphate isomerase:hypothetical protein:->->:1270379..1270507 129 actttaaactcttgattaaacttgttttctacttgaaaaaatgagaataaaatgctagtatcttaagagctgtgatagttgtttagctttacagtataatgaaataacttaaattggagggttattaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1236:TDE1237|TDE1236:TDE1237:triosephosphate isomerase:hypothetical protein:->->:1270379..1270507 129 actttaaactcttgattaaacttgttttctacttgaaaaaatgagaataaaatgctagtatcttaagagctgtgatagttgtttagctttacagtataatgaaataacttaaattggagggttattaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1236:TDE1237|TDE1236:TDE1237:triosephosphate isomerase:hypothetical protein:->->:1270379..1270507 129 actttaaactcttgattaaacttgttttctacttgaaaaaatgagaataaaatgctagtatcttaagagctgtgatagttgtttagctttacagtataatgaaataacttaaattggagggttattaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actttaaactcttgattaaacttgttttctacttgaaaaaatgagaataaaatgctagtatcttaagagctgtgatagttgtttagctttacagtataatgaaataacttaaattggagggttattaag Predict ORF larger than 30AA ================================================ actttaaactcttgattaaacttgttttctacttgaaaaaatgagaataaaatgctagtatcttaagagctgtgatagttgtttagctttacagtataatgaaataacttaaattggagggttattaag 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: 83 Start: 32 End: 61 ...............................CTTGAAAAAATGAGAATAAAATGCTAGTAT.................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 71 End: 100 ......................................................................TGTGATAGTTGTTTAGCTTTACAGTATAAT............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ actttaaactcttgattaaacttgttttctacttgaaaaaatgagaataaaatgctagtatcttaagagctgtgatagttgtttagctttacagtataatgaaataacttaaattggagggttattaag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1236:TDE1237|TDE1236:TDE1237:triosephosphate isomerase:hypothetical protein:->->:1270379..1270507 129 actttaaactcttgattaaacttgttttctacttgaaaaaatgagaataaaatgctagtatcttaagagctgtgatagttgtttagctttacagtataatgaaataacttaaattggagggttattaag Intra-Species Hit: Count: 1 Min: 1 Max: 129 Len: 129 Subject: NC_002967_TDE1236_TDE1237|triosephosphate isomerase:hypothetical protein|POSITIVE:POSITIVE|[1270379,1270507]|129 HSP 1 e-value: 2.0E-67 bit: 256.0 Len: 129 Query Start:1 Query End:129 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 actttaaactcttgattaaacttgttttctacttgaaaaaatgagaataaaatgctagtatcttaagagctgtgatagttgtttagctttacagtataatgaaataacttaaattggagggttattaag actttaaactcttgattaaacttgttttctacttgaaaaaatgagaataaaatgctagtatcttaagagctgtgatagttgtttagctttacagtataatgaaataacttaaattggagggttattaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUUAAACUCUUGAUUAAACUUGUUUUCUACUUGAAAAAAUGAGAAUAAAAUGCUAGUAUCUUAAGAGCUGUGAUAGUUGUUUAGCUUUACAGUAUAAUGAAAUAACUUAAAUUGGAGGGUUAUUAAG ......(((((((.(......((((((((...((....))..))))))))..................(((((((.(((......))))))))))...................).)))))))...... (-20.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUAAUAACCCUCCAAUUUAAGUUAUUUCAUUAUACUGUAAAGCUAAACAACUAUCACAGCUCUUAAGAUACUAGCAUUUUAUUCUCAUUUUUUCAAGUAGAAAACAAGUUUAAUCAAGAGUUUAAAGU ...((((((............))))))........((....((((.............))))....))........((((((..(((...(((((.....)))))...(......)..)))..)))))) ( -8.62) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 230 118 71 99 48 NC_002967:TDE0017|5end_hypothetical_protein_22936..23166_NEGATIVE 227 92 52 94 43 NC_002967:TDE2428|5end_ribosomal_protein_L33_2456292..2456522_NEGATIVE 225 90 43 206 158 NC_002967:TDE0938|5end_hypothetical_protein_962174..962404_NEGATIVE 222 64 21 103 57 NC_002967:TDE2240|5end_hypothetical_protein_2278422..2278652_NEGATIVE 216 96 51 161 108 NC_002967:TDE2006|5end_hypothetical_protein_2024421..2024651_POSITIVE 212 89 60 127 96 NC_002967:TDE1285|5end_flagellar_motor_switch_protein_FliG_,_putative_1320924..1321154_POSITIVE 210 90 53 160 122 NC_002967:TDE2422|5end_ribosomal_protein_L7/L12_2453300..2453530_NEGATIVE 210 85 43 190 143 NC_002967:TDE2380|5end_hypothetical_protein_2409819..2410049_POSITIVE 208 91 52 90 42 NC_002967:TDE2572|5end_CDP-diacylglycerol--glycerol-3-phosphate_3-phosphatidyltransferase_2598738..2598968_NEGATIVE 202 108 65 46 1 NC_002967:TDE2672|5end_TPR_domain_protein_2710210..2710440_POSITIVE 201 97 54 73 21 NC_002967:TDE1311|5end_ABC_transporter,_ATP-binding/permease_protein_1347371..1347601_POSITIVE 201 95 51 189 149 NC_002967:TDE0898|5end_hypothetical_protein_915878..916108_POSITIVE 199 90 44 141 90 NC_002967:TDE2137|5end_hypothetical_protein_2166125..2166355_POSITIVE 198 77 31 62 10 NC_002967:TDE2729|5end_hypothetical_protein_2786457..2786687_NEGATIVE 197 102 67 137 102 NC_002967:TDE1384|5end_cadmium-translocating_P-type_ATPase_1422765..1422995_POSITIVE 196 98 53 103 59 NC_002967:TDE1444|5end_metallo-beta-lactamase_family_protein_1491004..1491234_NEGATIVE 193 96 69 32 4 NC_002967:TDE0400|5end_transcriptional_regulator,_LysR_family_451803..452033_NEGATIVE 192 87 41 181 142 NC_002967:TDE1542|5end_hypothetical_protein_1585857..1586087_POSITIVE 192 96 53 191 144 NC_002967:TDE0301|5end_tetracenomycin_polyketide_synthesis_O-methyltransferase_TcmP,_putative_332347..332577_POSITIVE 191 76 32 190 136 NC_002967:TDE2618|5end_PHP_domain_protein_2659392..2659622_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 216 96 51 70 17 NC_002967:TDE2005|3end_hypothetical_protein_2024410..2024560_POSITIVE 212 89 60 46 15 NC_002967:TDE1284|3end_methyl-accepting_chemotaxis_protein,_putative_1320923..1321073_POSITIVE 210 90 53 43 5 NC_002967:TDE2423|3end_ribosomal_protein_L10_2453417..2453567_NEGATIVE 197 102 67 143 108 NC_002967:TDE1383|3end_hypothetical_protein_1422851..1423001_POSITIVE 194 97 66 149 113 NC_002967:TDE0428|3end_TPR_domain_protein_484453..484603_NEGATIVE 193 89 41 60 6 NC_002967:TDE0576|3end_glutamyl-tRNA(Gln)_amidotransferase,_A_subunit_607726..607876_NEGATIVE 193 93 54 136 98 NC_002967:TDE0280|3end_PIN_domain_protein_309895..310045_NEGATIVE 192 96 53 117 70 NC_002967:TDE0300|3end_leucyl_aminopeptidase_332353..332503_POSITIVE 189 90 54 114 76 NC_002967:TDE2299|3end_apolipoprotein_N-acyltransferase_2339937..2340087_POSITIVE 184 96 51 148 107 NC_002967:TDE2708|3end_hypothetical_protein_2755136..2755286_NEGATIVE 184 90 61 150 119 NC_002967:TDE2117|3end_hypothetical_protein_2149175..2149325_POSITIVE 183 98 53 59 21 NC_002967:TDE1174|3end_hypothetical_protein_1202651..1202801_NEGATIVE 182 98 61 131 100 NC_002967:TDE2298|3end_galactokinase,_putative_2337113..2337263_NEGATIVE 178 93 51 69 23 NC_002967:TDE2254|3end_hypothetical_protein_2291445..2291595_NEGATIVE 178 47 2 89 49 NC_002967:TDE2166|3end_hydrogenase_nickel_insertion_protein_HypA_2197743..2197893_NEGATIVE 178 95 55 71 19 NC_002967:TDE1795|3end_funZ_protein,_putative_1833063..1833213_NEGATIVE 178 90 41 145 93 NC_002967:TDE0168|3end_transcriptional_regulator,_GntR_family_196667..196817_NEGATIVE 177 89 52 70 32 NC_002967:TDE0550|3end_hypothetical_protein_587370..587520_NEGATIVE 176 95 65 130 94 NC_002967:TDE2740|3end_type_I_restriction-modification_system,_S_subunit,_truncation_2795770..2795920_POSITIVE 176 96 54 128 84 NC_002967:TDE2739|3end_hypothetical_protein_2795169..2795319_POSITIVE