Origin IGS: tttaagactccttgttataggaaacctcgaaaaacgaaaagtttttcgaggtttcccttatatttatttacgacgttttttagatttacatttcagccgtttttaatatacttattttagcgcatttagtccactgttttttatgattctcc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggagaatcataaaaaacagtggactaaatgcgctaaaataagtatattaaaaacggctgaaatgtaaatctaaaaaacgtcgtaaataaatataagggaaacctcgaaaaacttttcgtttttcgaggtttcctataacaaggagtcttaaa Mask Tandem Repeat Region ================================================ tttaagactccttgttataggaaacctcgaaaaacgaaaagtttttcgaggtttcccttatatttatttacgacgttttttagatttacatttcagccgtttttaatatacttattttagcgcatttagtccactgttttttatgattctcc Find is-nt database================================================ Query_seq: TDE0346:TDE0347|TDE0346:TDE0347:protease PrtB:methyl-accepting chemotaxis protein DmcA:<-<-:387988..388139 152 tttaagactccttgttataggaaacctcgaaaaacgaaaagtttttcgaggtttcccttatatttatttacgacgttttttagatttacatttcagccgtttttaatatacttattttagcgcatttagtccactgttttttatgattctcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0346:TDE0347|TDE0346:TDE0347:protease PrtB:methyl-accepting chemotaxis protein DmcA:<-<-:387988..388139 152 tttaagactccttgttataggaaacctcgaaaaacgaaaagtttttcgaggtttcccttatatttatttacgacgttttttagatttacatttcagccgtttttaatatacttattttagcgcatttagtccactgttttttatgattctcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0346:TDE0347|TDE0346:TDE0347:protease PrtB:methyl-accepting chemotaxis protein DmcA:<-<-:387988..388139 152 tttaagactccttgttataggaaacctcgaaaaacgaaaagtttttcgaggtttcccttatatttatttacgacgttttttagatttacatttcagccgtttttaatatacttattttagcgcatttagtccactgttttttatgattctcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttaagactccttgttataggaaacctcgaaaaacgaaaagtttttcgaggtttcccttatatttatttacgacgttttttagatttacatttcagccgtttttaatatacttattttagcgcatttagtccactgttttttatgattctcc Predict ORF larger than 30AA ================================================ tttaagactccttgttataggaaacctcgaaaaacgaaaagtttttcgaggtttcccttatatttatttacgacgttttttagatttacatttcagccgtttttaatatacttattttagcgcatttagtccactgttttttatgattctcc 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================================================ tttaagactccttgttataggaaacctcgaaaaacgaaaagtttttcgaggtttcccttatatttatttacgacgttttttagatttacatttcagccgtttttaatatacttattttagcgcatttagtccactgttttttatgattctcc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -16.0 Tail_Score: -3.81557 Start: 16 End: 60 Full_Region: TTTAAGACTCCTTGT TATAGGAAACCTCGAAAAAC GAAAA GTTTTTCGAGGTTTCCCTTA TATTTATTTACGACG ...............TATAGGAAACCTCGAAAAACGAAAAGTTTTTCGAGGTTTCCCTTA............................................................................................ TransTerm Strand: + Conf: 100 HP_score: -12.8 Tail_Score: -4.42464 Start: 16 End: 62 Full_Region: TTTAAGACTCCTTGT TATAGGAAACCTCGAAAAAC GAAAA GTTTTTCGAGGTTTCCCTTATA TTTATTTACGACGTT ...............TATAGGAAACCTCGAAAAACGAAAAGTTTTTCGAGGTTTCCCTTATA.......................................................................................... TransTerm Strand: - Conf: 100 HP_score: -13.9 Tail_Score: -3.83026 Start: 25 End: 51 Full_Region: taaatataagggaaa cctcgaaaaac ttttc gtttttcgagg tttcctataacaagg ........................cctcgaaaaacttttcgtttttcgagg..................................................................................................... TransTerm Strand: - Conf: 70 HP_score: -5.3 Tail_Score: -4.64657 Start: 35 End: 48 Full_Region: atataagggaaacct cgaaa aact tttcg tttttcgaggtttcc ..................................cgaaaaacttttcg........................................................................................................ Find igs database================================================ Query_seq: TDE0346:TDE0347|TDE0346:TDE0347:protease PrtB:methyl-accepting chemotaxis protein DmcA:<-<-:387988..388139 152 tttaagactccttgttataggaaacctcgaaaaacgaaaagtttttcgaggtttcccttatatttatttacgacgttttttagatttacatttcagccgtttttaatatacttattttagcgcatttagtccactgttttttatgattctcc Intra-Species Hit: Count: 1 Min: 1 Max: 152 Len: 152 Subject: NC_002967_TDE0346_TDE0347|protease PrtB:methyl-accepting chemotaxis protein DmcA|NEGATIVE:NEGATIVE|[387988,388139]|152 HSP 1 e-value: 2.0E-14 bit: 79.8 Len: 40 Query Start:1 Query End:40 Subject Strand: POSITIVE Subject Start: 1 Subject End: 40 tttaagactccttgttataggaaacctcgaaaaacgaaaa................................................................................................................ tttaagactccttgttataggaaacctcgaaaaacgaaaa................................................................................................................ HSP 2 e-value: 4.0E-10 bit: 65.9 Len: 33 Query Start:120 Query End:152 Subject Strand: POSITIVE Subject Start: 120 Subject End: 152 .......................................................................................................................gcgcatttagtccactgttttttatgattctcc .......................................................................................................................gcgcatttagtccactgttttttatgattctcc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAAGACUCCUUGUUAUAGGAAACCUCGAAAAACGAAAAGUUUUUCGAGGUUUCCCUUAUAUUUAUUUACGACGUUUUUUAGAUUUACAUUUCAGCCGUUUUUAAUAUACUUAUUUUAGCGCAUUUAGUCCACUGUUUUUUAUGAUUCUCC ...(((((...........((((((((((((((((.....))))))))))))))))...............(((........((........)).((.(((...((((....))))..))))).....)))....)))))............ (-33.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAGAAUCAUAAAAAACAGUGGACUAAAUGCGCUAAAAUAAGUAUAUUAAAAACGGCUGAAAUGUAAAUCUAAAAAACGUCGUAAAUAAAUAUAAGGGAAACCUCGAAAAACUUUUCGUUUUUCGAGGUUUCCUAUAACAAGGAGUCUUAAA .((((.((........((((.(....((((..((......))..)))).....).))))....................................(((((((((((((((((.....)))))))))))))))))........)).))))... (-37.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 806 60 11 151 102 NC_002967:TDE0346|5end_protease_PrtB_387897..388127_NEGATIVE 307 59 19 39 1 NC_002967:TDE2027|5end_hypothetical_protein_2052649..2052879_POSITIVE 307 56 13 54 12 NC_002967:TDE0331|5end_hypothetical_protein_370943..371173_NEGATIVE 304 55 20 209 176 NC_002967:TDE0332|5end_transcriptional_regulator,_TetR_family_370940..371170_POSITIVE 288 59 11 153 109 NC_002967:TDE2256|5end_hypothetical_protein_2293387..2293617_NEGATIVE 287 49 5 142 97 NC_002967:TDE2400|5end_50S_ribosomal_protein_L34_2426327..2426557_NEGATIVE 273 50 4 153 107 NC_002967:TDE0744|5end_thioredoxin_779844..780074_POSITIVE 254 59 11 203 153 NC_002967:TDE0943|5end_hypothetical_protein_965983..966213_POSITIVE 241 94 54 132 91 NC_002967:TDE2192|5end_threonine_synthase_2227761..2227991_POSITIVE 237 140 94 224 175 NC_002967:TDE1895|5end_GTP-binding_protein_Era_1914963..1915193_POSITIVE 236 60 11 216 166 NC_002967:TDE0853|5end_ribosomal_protein_S9_875473..875703_POSITIVE 230 55 20 108 75 NC_002967:TDE0629|5end_chaperone_protein_DnaJ_662587..662817_POSITIVE 228 140 91 66 13 NC_002967:TDE1601|5end_transcriptional_regulator,_TetR_family_1653036..1653266_NEGATIVE 225 58 11 224 182 NC_002967:TDE0501|5end_hypothetical_protein_555312..555542_NEGATIVE 225 60 15 147 105 NC_002967:TDE0467|5end_hypothetical_protein_520430..520660_NEGATIVE 224 81 42 50 11 NC_002967:TDE0375|5end_ABC_transporter,_ATP-binding_protein_430147..430377_NEGATIVE 222 141 111 221 193 NC_002967:TDE2187|5end_ParB-like_nuclease_domain_protein_2221548..2221778_NEGATIVE 219 67 38 44 8 NC_002967:TDE2538|5end_hypothetical_protein_2563785..2564015_POSITIVE 213 121 81 114 74 NC_002967:TDE0842|5end_cytoplasmic_filament_protein_A_861715..861945_POSITIVE 211 140 95 210 169 NC_002967:TDE2105|5end_hypothetical_protein_2131484..2131714_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 360 59 12 87 44 NC_002967:TDE0356|3end_hypothetical_protein_399732..399882_NEGATIVE 344 69 22 78 33 NC_002967:TDE0186|3end_hypothetical_protein_222373..222523_NEGATIVE 303 55 17 62 25 NC_002967:TDE2270|3end_methyl-accepting_chemotaxis_protein_2306280..2306430_NEGATIVE 294 69 23 96 51 NC_002967:TDE0151|3end_integral_membrane_protein,_YeeE/YedE_family_171845..171995_NEGATIVE 290 69 22 96 52 NC_002967:TDE0525|3end_hypothetical_protein_571163..571313_POSITIVE 280 60 19 87 47 NC_002967:TDE0185|3end_ABC_transporter,_ATP-binding_protein,_HlyB_family_222335..222485_POSITIVE 271 52 13 48 9 NC_002967:TDE1734|3end_exodeoxyribonuclease_III_1789463..1789613_POSITIVE 254 56 18 89 51 NC_002967:TDE1264|3end_hypothetical_protein_1298152..1298302_NEGATIVE 254 59 11 79 29 NC_002967:TDE0942|3end_long-chain-fatty-acid--CoA_ligase,_putative_965939..966089_POSITIVE 241 60 16 93 51 NC_002967:TDE1992|3end_OmpA_family_protein_2010902..2011052_POSITIVE 239 60 20 93 49 NC_002967:TDE2029|3end_hydrolase,_TatD_family_2057148..2057298_NEGATIVE 238 59 21 37 1 NC_002967:TDE2257|3end_5'-nucleotidase_family_protein_2293503..2293653_NEGATIVE 236 54 14 82 42 NC_002967:TDE1993|3end_aspartate_ammonia-lyase,_putative_2010917..2011067_NEGATIVE 233 52 13 151 113 NC_002967:TDE0331|3end_hypothetical_protein_370842..370992_NEGATIVE 230 55 20 70 37 NC_002967:TDE0628|3end_molecular_chaperone_DnaK_662629..662779_POSITIVE 230 59 14 84 42 NC_002967:TDE0150|3end_ribonuclease_BN-like_family_protein_171825..171975_POSITIVE 228 99 51 104 58 NC_002967:TDE0852|3end_50S_ribosomal_protein_L13_875527..875677_POSITIVE 225 60 15 77 35 NC_002967:TDE0468|3end_hypothetical_protein_520500..520650_NEGATIVE 223 58 19 84 46 NC_002967:TDE1263|3end_hypothetical_protein_1298136..1298286_POSITIVE 221 59 14 117 73 NC_002967:TDE2147|3end_lipoprotein,_putative_2184036..2184186_NEGATIVE