Origin IGS: gttccctcctatggacacatttctgaggcccgcattttctgcgagccggagttttcatagaatatcaaaaaatactatcttagtcaatacccggcataaaaccggctaaacctagcacttcatcatcccgcatactgtaggct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agcctacagtatgcgggatgatgaagtgctaggtttagccggttttatgccgggtattgactaagatagtattttttgatattctatgaaaactccggctcgcagaaaatgcgggcctcagaaatgtgtccataggagggaac Mask Tandem Repeat Region ================================================ gttccctcctatggacacatttctgaggcccgcattttctgcgagccggagttttcatagaatatcaaaaaatactatcttagtcaatacccggcataaaaccggctaaacctagcacttcatcatcccgcatactgtaggct Find is-nt database================================================ Query_seq: TDE1678:TDE1679|TDE1678:TDE1679:ribosomal protein S6:ATP synthase subunit K:<-<-:1730574..1730716 143 gttccctcctatggacacatttctgaggcccgcattttctgcgagccggagttttcatagaatatcaaaaaatactatcttagtcaatacccggcataaaaccggctaaacctagcacttcatcatcccgcatactgtaggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1678:TDE1679|TDE1678:TDE1679:ribosomal protein S6:ATP synthase subunit K:<-<-:1730574..1730716 143 gttccctcctatggacacatttctgaggcccgcattttctgcgagccggagttttcatagaatatcaaaaaatactatcttagtcaatacccggcataaaaccggctaaacctagcacttcatcatcccgcatactgtaggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1678:TDE1679|TDE1678:TDE1679:ribosomal protein S6:ATP synthase subunit K:<-<-:1730574..1730716 143 gttccctcctatggacacatttctgaggcccgcattttctgcgagccggagttttcatagaatatcaaaaaatactatcttagtcaatacccggcataaaaccggctaaacctagcacttcatcatcccgcatactgtaggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gttccctcctatggacacatttctgaggcccgcattttctgcgagccggagttttcatagaatatcaaaaaatactatcttagtcaatacccggcataaaaccggctaaacctagcacttcatcatcccgcatactgtaggct Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 11 End: 106 .......... M D T F L R P A F S A S R S F H R I S K N T I L V N T R H K T G ..................................... gttccctcctatggacacatttctgaggcccgcattttctgcgagccggagttttcatagaatatcaaaaaatactatcttagtcaatacccggcataaaaccggctaaacctagcacttcatcatcccgcatactgtaggct 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: 84 Start: 59 End: 88 ..........................................................ATTGACTAAGATAGTATTTTTTGATATTCT....................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gttccctcctatggacacatttctgaggcccgcattttctgcgagccggagttttcatagaatatcaaaaaatactatcttagtcaatacccggcataaaaccggctaaacctagcacttcatcatcccgcatactgtaggct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1678:TDE1679|TDE1678:TDE1679:ribosomal protein S6:ATP synthase subunit K:<-<-:1730574..1730716 143 gttccctcctatggacacatttctgaggcccgcattttctgcgagccggagttttcatagaatatcaaaaaatactatcttagtcaatacccggcataaaaccggctaaacctagcacttcatcatcccgcatactgtaggct Intra-Species Hit: Count: 1 Min: 1 Max: 143 Len: 143 Subject: NC_002967_TDE1678_TDE1679|ribosomal protein S6:ATP synthase subunit K|NEGATIVE:NEGATIVE|[1730574,1730716]|143 HSP 1 e-value: 8.0E-76 bit: 283.0 Len: 143 Query Start:1 Query End:143 Subject Strand: POSITIVE Subject Start: 1 Subject End: 143 gttccctcctatggacacatttctgaggcccgcattttctgcgagccggagttttcatagaatatcaaaaaatactatcttagtcaatacccggcataaaaccggctaaacctagcacttcatcatcccgcatactgtaggct gttccctcctatggacacatttctgaggcccgcattttctgcgagccggagttttcatagaatatcaaaaaatactatcttagtcaatacccggcataaaaccggctaaacctagcacttcatcatcccgcatactgtaggct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUCCCUCCUAUGGACACAUUUCUGAGGCCCGCAUUUUCUGCGAGCCGGAGUUUUCAUAGAAUAUCAAAAAAUACUAUCUUAGUCAAUACCCGGCAUAAAACCGGCUAAACCUAGCACUUCAUCAUCCCGCAUACUGUAGGCU ((..((......))..))........((((..((.....((((.(((((.((......(((................)))........))))))).........((((....))))............))))...))..)))) (-27.73) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCCUACAGUAUGCGGGAUGAUGAAGUGCUAGGUUUAGCCGGUUUUAUGCCGGGUAUUGACUAAGAUAGUAUUUUUUGAUAUUCUAUGAAAACUCCGGCUCGCAGAAAAUGCGGGCCUCAGAAAUGUGUCCAUAGGAGGGAAC ..((..((((((.(((.((((....(.((((....)))))....)))).))).))))))......................(((((((........((((((((.....)))))))).((....))....))))))).))... (-42.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1059 50 1 141 92 NC_002967:TDE1678|5end_ribosomal_protein_S6_1730483..1730713_NEGATIVE 348 139 91 49 16 NC_002967:TDE2060|5end_hypothetical_protein_2086521..2086751_POSITIVE 340 62 22 190 137 NC_002967:TDE2044|5end_lipoprotein,_putative_2074616..2074846_NEGATIVE 313 39 1 43 4 NC_002967:TDE1405|5end_phosphoribosylformylglycinamidine_synthetase_I_1448674..1448904_NEGATIVE 313 66 21 148 102 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 311 50 2 229 165 NC_002967:TDE2259|5end_hypothetical_protein_2297237..2297467_NEGATIVE 311 49 4 53 1 NC_002967:TDE0573|5end_hypothetical_protein_604681..604911_POSITIVE 310 70 26 109 46 NC_002967:TDE2382|5end_cobinamide_kinase/cobinamide_phosphate_guanyltransferase_2412278..2412508_POSITIVE 308 133 91 167 122 NC_002967:TDE2596|5end_hypothetical_protein_2632039..2632269_NEGATIVE 308 49 4 62 11 NC_002967:TDE1638|5end_dephospho-CoA_kinase,_putative_1688882..1689112_POSITIVE 305 53 18 139 89 NC_002967:TDE1566|5end_hypothetical_protein_1617822..1618052_POSITIVE 299 59 27 56 5 NC_002967:TDE0456|5end_pyridoxine_biosynthesis_protein_513384..513614_NEGATIVE 297 67 26 217 172 NC_002967:TDE2235|5end_methylaspartate_ammonia-lyase_2274588..2274818_NEGATIVE 293 64 21 70 17 NC_002967:TDE2505|5end_hypothetical_protein_2530125..2530355_POSITIVE 292 49 2 172 137 NC_002967:TDE2714|5end_hypothetical_protein_2772618..2772848_NEGATIVE 292 49 10 52 19 NC_002967:TDE1374|5end_hypothetical_protein_1417998..1418228_NEGATIVE 292 49 10 209 176 NC_002967:TDE1373|5end_HD_domain_protein_1417841..1418071_NEGATIVE 290 55 21 190 148 NC_002967:TDE2607|5end_hypothetical_protein_2648586..2648816_POSITIVE 290 130 82 74 19 NC_002967:TDE0006|5end_Snf2_family_protein_9694..9924_NEGATIVE 289 58 14 110 66 NC_002967:TDE1926|5end_hypothetical_protein_1942495..1942725_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 336 139 91 124 65 NC_002967:TDE2422|3end_ribosomal_protein_L7/L12_2452911..2453061_NEGATIVE 313 39 1 40 1 NC_002967:TDE1406|3end_hypothetical_protein_1448677..1448827_NEGATIVE 313 66 21 146 100 NC_002967:TDE0956|3end_hypothetical_protein_980330..980480_POSITIVE 308 49 4 62 11 NC_002967:TDE1637|3end_DNA_polymerase_I_1688962..1689112_POSITIVE 297 67 26 145 100 NC_002967:TDE2236|3end_methylaspartate_mutase,_E_subunit_2274660..2274810_NEGATIVE 295 56 19 44 6 NC_002967:TDE1672|3end_ATP-dependent_Clp_protease,_proteolytic_subunit_ClpP_1726965..1727115_POSITIVE 290 55 21 75 33 NC_002967:TDE2606|3end_urocanate_hydratase_2648551..2648701_POSITIVE 290 47 4 62 19 NC_002967:TDE2436|3end_hypothetical_protein_2467446..2467596_POSITIVE 289 58 14 140 96 NC_002967:TDE1925|3end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_1942605..1942755_POSITIVE 288 51 23 60 27 NC_002967:TDE2250|3end_hypothetical_protein_2289409..2289559_POSITIVE 281 50 5 74 10 NC_002967:TDE2674|3end_hypothetical_protein_2712465..2712615_NEGATIVE 281 50 1 121 74 NC_002967:TDE0322|3end_regulatory_protein,_P-II_family_355106..355256_NEGATIVE 278 48 7 57 1 NC_002967:TDE2238|3end_hypothetical_protein_2276545..2276695_POSITIVE 278 49 4 151 103 NC_002967:TDE1719|3end_transcriptional_regulator,_MarR_family_1774546..1774696_POSITIVE 277 47 11 51 18 NC_002967:TDE0796|3end_histidinol_phosphate_phosphatase_HisJ_family_protein_820946..821096_POSITIVE 273 51 11 149 115 NC_002967:TDE1198|3end_S-adenosyl-methyltransferase_MraW_1231419..1231569_POSITIVE 270 66 21 146 100 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 270 69 21 98 38 NC_002967:TDE1791|3end_hypothetical_protein_1828308..1828458_NEGATIVE 269 48 4 89 42 NC_002967:TDE1736|3end_ferredoxin,_2(4Fe-4S)_1790158..1790308_POSITIVE 269 50 1 113 61 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE