Origin IGS: gtagttataaaaaggaacctctaagagcttcagttttttagaggttcccatatctttataagatggaaagatgtttgaaatgggccttgcaatatgcagcaaaaccgtgtatactaaacacca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tggtgtttagtatacacggttttgctgcatattgcaaggcccatttcaaacatctttccatcttataaagatatgggaacctctaaaaaactgaagctcttagaggttcctttttataactac Mask Tandem Repeat Region ================================================ gtagttataaaaaggaacctctaagagcttcagttttttagaggttcccatatctttataagatggaaagatgtttgaaatgggccttgcaatatgcagcaaaaccgtgtatactaaacacca Find is-nt database================================================ Query_seq: TDE0942:TDE0943|TDE0942:TDE0943:long-chain-fatty-acid--CoA ligase, putative:hypothetical protein:->->:966000..966122 123 gtagttataaaaaggaacctctaagagcttcagttttttagaggttcccatatctttataagatggaaagatgtttgaaatgggccttgcaatatgcagcaaaaccgtgtatactaaacacca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0942:TDE0943|TDE0942:TDE0943:long-chain-fatty-acid--CoA ligase, putative:hypothetical protein:->->:966000..966122 123 gtagttataaaaaggaacctctaagagcttcagttttttagaggttcccatatctttataagatggaaagatgtttgaaatgggccttgcaatatgcagcaaaaccgtgtatactaaacacca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0942:TDE0943|TDE0942:TDE0943:long-chain-fatty-acid--CoA ligase, putative:hypothetical protein:->->:966000..966122 123 gtagttataaaaaggaacctctaagagcttcagttttttagaggttcccatatctttataagatggaaagatgtttgaaatgggccttgcaatatgcagcaaaaccgtgtatactaaacacca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtagttataaaaaggaacctctaagagcttcagttttttagaggttcccatatctttataagatggaaagatgtttgaaatgggccttgcaatatgcagcaaaaccgtgtatactaaacacca Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 1 End: 102 Y N Y F P V E L L K L K K S T G M D K Y S P F I N S I P R A I H L M ..................... gtagttataaaaaggaacctctaagagcttcagttttttagaggttcccatatctttataagatggaaagatgtttgaaatgggccttgcaatatgcagcaaaaccgtgtatactaaacacca 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: 86 End: 115 .....................................................................................CTTGCAATATGCAGCAAAACCGTGTATACT........ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtagttataaaaaggaacctctaagagcttcagttttttagaggttcccatatctttataagatggaaagatgtttgaaatgggccttgcaatatgcagcaaaaccgtgtatactaaacacca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0942:TDE0943|TDE0942:TDE0943:long-chain-fatty-acid--CoA ligase, putative:hypothetical protein:->->:966000..966122 123 gtagttataaaaaggaacctctaagagcttcagttttttagaggttcccatatctttataagatggaaagatgtttgaaatgggccttgcaatatgcagcaaaaccgtgtatactaaacacca Intra-Species Hit: Count: 1 Min: 1 Max: 123 Len: 123 Subject: NC_002967_TDE0942_TDE0943|long-chain-fatty-acid--CoA ligase, putative:hypothetical protein|POSITIVE:POSITIVE|[966000,966122]|123 HSP 1 e-value: 6.0E-64 bit: 244.0 Len: 123 Query Start:1 Query End:123 Subject Strand: POSITIVE Subject Start: 1 Subject End: 123 gtagttataaaaaggaacctctaagagcttcagttttttagaggttcccatatctttataagatggaaagatgtttgaaatgggccttgcaatatgcagcaaaaccgtgtatactaaacacca gtagttataaaaaggaacctctaagagcttcagttttttagaggttcccatatctttataagatggaaagatgtttgaaatgggccttgcaatatgcagcaaaaccgtgtatactaaacacca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAGUUAUAAAAAGGAACCUCUAAGAGCUUCAGUUUUUUAGAGGUUCCCAUAUCUUUAUAAGAUGGAAAGAUGUUUGAAAUGGGCCUUGCAAUAUGCAGCAAAACCGUGUAUACUAAACACCA .((((.(((....(((((((((((((((....).)))))))))))))).((((((((.........)))))))).....((((...((((........))))..)))).)))))))....... (-31.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGGUGUUUAGUAUACACGGUUUUGCUGCAUAUUGCAAGGCCCAUUUCAAACAUCUUUCCAUCUUAUAAAGAUAUGGGAACCUCUAAAAAACUGAAGCUCUUAGAGGUUCCUUUUUAUAACUAC .(((((((.(.......((((((((........)))))))).....))))))))........((((((((....((((((((((((.............)))))))))))))))))))).... (-34.42) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 436 48 8 108 65 NC_002967:TDE0629|5end_chaperone_protein_DnaJ_662587..662817_POSITIVE 403 49 13 151 116 NC_002967:TDE2256|5end_hypothetical_protein_2293387..2293617_NEGATIVE 396 51 14 56 20 NC_002967:TDE0331|5end_hypothetical_protein_370943..371173_NEGATIVE 348 48 15 159 126 NC_002967:TDE2062|5end_hypothetical_protein_2088344..2088574_NEGATIVE 325 48 14 209 176 NC_002967:TDE0332|5end_transcriptional_regulator,_TetR_family_370940..371170_POSITIVE 316 57 13 46 1 NC_002967:TDE2027|5end_hypothetical_protein_2052649..2052879_POSITIVE 312 88 49 208 158 NC_002967:TDE2690|5end_hypothetical_protein_2728898..2729128_NEGATIVE 293 117 73 62 14 NC_002967:TDE0006|5end_Snf2_family_protein_9694..9924_NEGATIVE 287 59 12 158 111 NC_002967:TDE2461|5end_selenide,_water_dikinase_(selenocysteine-containing)_2488260..2488490_NEGATIVE 276 49 4 148 105 NC_002967:TDE0346|5end_protease_PrtB_387897..388127_NEGATIVE 269 49 13 157 120 NC_002967:TDE1269|5end_hypothetical_protein_1304522..1304752_NEGATIVE 265 44 18 164 139 NC_002967:TDE1623|5end_hypothetical_protein_1671980..1672210_NEGATIVE 264 70 23 129 93 NC_002967:TDE1983|5end_hypothetical_protein_1996339..1996569_NEGATIVE 263 108 62 187 140 NC_002967:TDE2625|5end_ABC_transporter,_ATP-binding/permease_protein_2666664..2666894_NEGATIVE 263 118 83 164 118 NC_002967:TDE1624|5end_glycine_dehydrogenase_subunit_2_1673519..1673749_NEGATIVE 261 48 2 167 125 NC_002967:TDE2693|5end_ankyrin_repeat_protein_2731133..2731363_POSITIVE 254 90 48 161 110 NC_002967:TDE0908|5end_ABC_transporter,_ATP-binding/permease_protein_925254..925484_POSITIVE 253 51 13 79 29 NC_002967:TDE2199|5end_racemase,_Asp/Glu/Hydantoin_family_2237150..2237380_NEGATIVE 252 56 12 103 57 NC_002967:TDE2212|5end_galactokinase_2252681..2252911_NEGATIVE 250 60 14 228 176 NC_002967:TDE1522|5end_citrate_lyase_ligase_1567780..1568010_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 541 57 14 105 54 NC_002967:TDE1264|3end_hypothetical_protein_1298152..1298302_NEGATIVE 458 56 14 86 49 NC_002967:TDE0185|3end_ABC_transporter,_ATP-binding_protein,_HlyB_family_222335..222485_POSITIVE 443 56 14 92 49 NC_002967:TDE2029|3end_hydrolase,_TatD_family_2057148..2057298_NEGATIVE 436 48 8 70 27 NC_002967:TDE0628|3end_molecular_chaperone_DnaK_662629..662779_POSITIVE 435 48 2 90 44 NC_002967:TDE1992|3end_OmpA_family_protein_2010902..2011052_POSITIVE 420 53 12 72 28 NC_002967:TDE0186|3end_hypothetical_protein_222373..222523_NEGATIVE 400 46 5 60 20 NC_002967:TDE2270|3end_methyl-accepting_chemotaxis_protein_2306280..2306430_NEGATIVE 387 49 15 35 1 NC_002967:TDE2257|3end_5'-nucleotidase_family_protein_2293503..2293653_NEGATIVE 360 48 14 77 43 NC_002967:TDE0942|3end_long-chain-fatty-acid--CoA_ligase,_putative_965939..966089_POSITIVE 348 48 15 73 40 NC_002967:TDE2063|3end_ferrous_iron_transport_protein_B_2088430..2088580_NEGATIVE 346 49 12 85 48 NC_002967:TDE0356|3end_hypothetical_protein_399732..399882_NEGATIVE 338 54 12 88 45 NC_002967:TDE1993|3end_aspartate_ammonia-lyase,_putative_2010917..2011067_NEGATIVE 333 49 1 83 35 NC_002967:TDE1263|3end_hypothetical_protein_1298136..1298286_POSITIVE 308 47 12 82 46 NC_002967:TDE0150|3end_ribonuclease_BN-like_family_protein_171825..171975_POSITIVE 303 47 10 61 22 NC_002967:TDE0860|3end_ribosomal_small_subunit_pseudouridine_synthase_A_881840..881990_POSITIVE 296 46 12 81 46 NC_002967:TDE0525|3end_hypothetical_protein_571163..571313_POSITIVE 287 59 12 113 66 NC_002967:TDE2462|3end_hypothetical_protein_2488305..2488455_NEGATIVE 271 47 12 81 47 NC_002967:TDE0151|3end_integral_membrane_protein,_YeeE/YedE_family_171845..171995_NEGATIVE 269 49 13 102 65 NC_002967:TDE1270|3end_hypothetical_protein_1304577..1304727_NEGATIVE 265 44 18 73 48 NC_002967:TDE1624|3end_glycine_dehydrogenase_subunit_2_1672071..1672221_NEGATIVE