Origin IGS: tttttatccttaaaataaaaccgccttgtgctcaagccctagctttttatagaacttgtaagctcggcacattaaggcggctttataagattttaagcgt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acgcttaaaatcttataaagccgccttaatgtgccgagcttacaagttctataaaaagctagggcttgagcacaaggcggttttattttaaggataaaaa Mask Tandem Repeat Region ================================================ tttttatccttaaaataaaaccgccttgtgctcaagccctagctttttatagaacttgtaagctcggcacattaaggcggctttataagattttaagcgt Find is-nt database================================================ Query_seq: TDE1291:TDE1292|TDE1291:TDE1292:HD domain protein:TldD/PmbA family protein:<-<-:1329304..1329403 100 tttttatccttaaaataaaaccgccttgtgctcaagccctagctttttatagaacttgtaagctcggcacattaaggcggctttataagattttaagcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1291:TDE1292|TDE1291:TDE1292:HD domain protein:TldD/PmbA family protein:<-<-:1329304..1329403 100 tttttatccttaaaataaaaccgccttgtgctcaagccctagctttttatagaacttgtaagctcggcacattaaggcggctttataagattttaagcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1291:TDE1292|TDE1291:TDE1292:HD domain protein:TldD/PmbA family protein:<-<-:1329304..1329403 100 tttttatccttaaaataaaaccgccttgtgctcaagccctagctttttatagaacttgtaagctcggcacattaaggcggctttataagattttaagcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttttatccttaaaataaaaccgccttgtgctcaagccctagctttttatagaacttgtaagctcggcacattaaggcggctttataagattttaagcgt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 6 End: 98 ..... M L K I K P P C A Q A L A F Y R T C K L G T L R R L Y K I L S .. tttttatccttaaaataaaaccgccttgtgctcaagccctagctttttatagaacttgtaagctcggcacattaaggcggctttataagattttaagcgt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttttatccttaaaataaaaccgccttgtgctcaagccctagctttttatagaacttgtaagctcggcacattaaggcggctttataagattttaagcgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1291:TDE1292|TDE1291:TDE1292:HD domain protein:TldD/PmbA family protein:<-<-:1329304..1329403 100 tttttatccttaaaataaaaccgccttgtgctcaagccctagctttttatagaacttgtaagctcggcacattaaggcggctttataagattttaagcgt Intra-Species Hit: Count: 1 Min: 1 Max: 100 Len: 100 Subject: NC_002967_TDE1291_TDE1292|HD domain protein:TldD/PmbA family protein|NEGATIVE:NEGATIVE|[1329304,1329403]|100 HSP 1 e-value: 2.0E-50 bit: 198.0 Len: 100 Query Start:1 Query End:100 Subject Strand: POSITIVE Subject Start: 1 Subject End: 100 tttttatccttaaaataaaaccgccttgtgctcaagccctagctttttatagaacttgtaagctcggcacattaaggcggctttataagattttaagcgt tttttatccttaaaataaaaccgccttgtgctcaagccctagctttttatagaacttgtaagctcggcacattaaggcggctttataagattttaagcgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUAUCCUUAAAAUAAAACCGCCUUGUGCUCAAGCCCUAGCUUUUUAUAGAACUUGUAAGCUCGGCACAUUAAGGCGGCUUUAUAAGAUUUUAAGCGU ........(((((((((((.((((((((((((((((..(((........)))..)))).......))))))...)))))).))))).....))))))... (-25.11) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGCUUAAAAUCUUAUAAAGCCGCCUUAAUGUGCCGAGCUUACAAGUUCUAUAAAAAGCUAGGGCUUGAGCACAAGGCGGUUUUAUUUUAAGGAUAAAAA ...((((((.....((((((((((((...((((((((((((...((((........)))).))))))).)))))))))))))))))))))))........ (-36.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 990 70 21 161 112 NC_002967:TDE1291|5end_HD_domain_protein_1329213..1329443_NEGATIVE 349 68 23 138 94 NC_002967:TDE0486|5end_hypothetical_protein_543612..543842_NEGATIVE 327 70 23 34 4 NC_002967:TDE0832|5end_hypothetical_protein_852549..852779_POSITIVE 325 68 21 43 6 NC_002967:TDE0322|5end_regulatory_protein,_P-II_family_355405..355635_NEGATIVE 294 69 22 74 23 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 289 80 33 85 38 NC_002967:TDE2182|5end_hypothetical_protein_2215035..2215265_NEGATIVE 289 78 37 163 113 NC_002967:TDE1157|5end_phage_terminase,_large_subunit,_putative_1193293..1193523_NEGATIVE 288 69 22 197 136 NC_002967:TDE1518|5end_permease,_putative_1564284..1564514_POSITIVE 287 69 21 165 111 NC_002967:TDE2491|5end_DNA_polymerase_domain_protein_2515499..2515729_NEGATIVE 286 62 21 79 33 NC_002967:TDE0878|5end_hypothetical_protein_899652..899882_POSITIVE 285 80 32 198 144 NC_002967:TDE2251|5end_uracil_permease_2289440..2289670_POSITIVE 284 60 20 50 8 NC_002967:TDE1744|5end_chromate_transport_protein_1799090..1799320_NEGATIVE 283 69 23 68 9 NC_002967:TDE1726|5end_polyA_polymerase_family_protein_1779546..1779776_POSITIVE 283 70 21 51 9 NC_002967:TDE0189|5end_hypothetical_protein_226460..226690_NEGATIVE 282 44 7 195 164 NC_002967:TDE2685|5end_flagellar_synthesis_regulator_FleN_2725783..2726013_NEGATIVE 280 80 34 56 19 NC_002967:TDE2736|5end_hypothetical_protein_2791812..2792042_NEGATIVE 280 69 26 177 124 NC_002967:TDE0050|5end_RNA_methyltransferase,_TrmH_family_60071..60301_NEGATIVE 278 69 23 172 121 NC_002967:TDE1492|5end_chemotaxis_protein_CheW_1537231..1537461_POSITIVE 278 69 21 71 30 NC_002967:TDE0239|5end_glycine_reductase_complex_protein_GrdD_272982..273212_NEGATIVE 273 48 17 38 13 NC_002967:TDE0573|5end_hypothetical_protein_604681..604911_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 378 99 51 67 22 NC_002967:TDE1402|3end_hypothetical_protein_1444515..1444665_POSITIVE 349 68 23 122 78 NC_002967:TDE0487|3end_ABC_transporter,_ATP-binding_protein_543628..543778_NEGATIVE 311 82 41 113 69 NC_002967:TDE1942|3end_hypothetical_protein_1959438..1959588_POSITIVE 294 69 22 102 51 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 286 68 21 58 8 NC_002967:TDE1488|3end_glyceraldehyde-3-phosphate_dehydrogenase,_type_I_1531604..1531754_NEGATIVE 285 80 32 87 33 NC_002967:TDE2250|3end_hypothetical_protein_2289409..2289559_POSITIVE 278 69 21 58 17 NC_002967:TDE0240|3end_glycine_reductase_complex_protein_GrdC_272995..273145_NEGATIVE 274 68 23 148 104 NC_002967:TDE1491|3end_chemotaxis_protein_CheA_1537294..1537444_POSITIVE 270 65 21 140 86 NC_002967:TDE1632|3end_citrate_lyase,_beta_subunit_1681569..1681719_NEGATIVE 270 71 31 146 110 NC_002967:TDE1331|3end_anaerobic_ribonucleoside_triphosphate_reductase_1368074..1368224_POSITIVE 270 68 21 75 25 NC_002967:TDE1026|3end_acyl_carrier_protein_1057618..1057768_POSITIVE 268 68 22 137 103 NC_002967:TDE1847|3end_hypothetical_protein_1875845..1875995_POSITIVE 267 98 66 82 43 NC_002967:TDE1926|3end_hypothetical_protein_1943663..1943813_POSITIVE 266 68 22 75 32 NC_002967:TDE2312|3end_hypothetical_protein_2349049..2349199_POSITIVE 265 90 41 117 61 NC_002967:TDE2778|3end_PspC_domain_protein_2829371..2829521_NEGATIVE 265 85 46 142 94 NC_002967:TDE2589|3end_putative_aminopeptidase_1_2625000..2625150_NEGATIVE 262 67 21 67 25 NC_002967:TDE2719|3end_hypothetical_protein_2777015..2777165_POSITIVE 262 83 43 45 1 NC_002967:TDE2321|3end_hypothetical_protein_2356948..2357098_NEGATIVE 260 84 41 110 55 NC_002967:TDE0745|3end_glycine_reductase_complex_selenoprotein_GrdA_780840..780990_POSITIVE 259 65 21 150 101 NC_002967:TDE2492|3end_hypothetical_protein_2515509..2515659_NEGATIVE