Origin IGS: ggactaatgcacaattttttaccggataatttaaaatcatctgcgtcttcctgtaagcttccttgacattacaagtatttgaatgtaatattgatagtataaatacttttattttaagaaggatact .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agtatccttcttaaaataaaagtatttatactatcaatattacattcaaatacttgtaatgtcaaggaagcttacaggaagacgcagatgattttaaattatccggtaaaaaattgtgcattagtcc Mask Tandem Repeat Region ================================================ ggactaatgcacaattttttaccggataatttaaaatcatctgcgtcttcctgtaagcttccttgacattacaagtatttgaatgtaatattgatagtataaatacttttattttaagaaggatact Find is-nt database================================================ Query_seq: TDE1911:TDE1912|TDE1911:TDE1912:hypothetical protein:redox-sensing transcriptional repressor Rex:<-->:1929189..1929315 127 ggactaatgcacaattttttaccggataatttaaaatcatctgcgtcttcctgtaagcttccttgacattacaagtatttgaatgtaatattgatagtataaatacttttattttaagaaggatact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1911:TDE1912|TDE1911:TDE1912:hypothetical protein:redox-sensing transcriptional repressor Rex:<-->:1929189..1929315 127 ggactaatgcacaattttttaccggataatttaaaatcatctgcgtcttcctgtaagcttccttgacattacaagtatttgaatgtaatattgatagtataaatacttttattttaagaaggatact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1911:TDE1912|TDE1911:TDE1912:hypothetical protein:redox-sensing transcriptional repressor Rex:<-->:1929189..1929315 127 ggactaatgcacaattttttaccggataatttaaaatcatctgcgtcttcctgtaagcttccttgacattacaagtatttgaatgtaatattgatagtataaatacttttattttaagaaggatact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggactaatgcacaattttttaccggataatttaaaatcatctgcgtcttcctgtaagcttccttgacattacaagtatttgaatgtaatattgatagtataaatacttttattttaagaaggatact Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: - Start: 2 End: 124 . V L A C N K V P Y N L I M Q T K R Y A E K V N C T N S H L I S L I F V K I K L L M ... ggactaatgcacaattttttaccggataatttaaaatcatctgcgtcttcctgtaagcttccttgacattacaagtatttgaatgtaatattgatagtataaatacttttattttaagaaggatact 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: 87 Start: 62 End: 91 .............................................................CTTGACATTACAAGTATTTGAATGTAATAT.................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ggactaatgcacaattttttaccggataatttaaaatcatctgcgtcttcctgtaagcttccttgacattacaagtatttgaatgtaatattgatagtataaatacttttattttaagaaggatact Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1911:TDE1912|TDE1911:TDE1912:hypothetical protein:redox-sensing transcriptional repressor Rex:<-->:1929189..1929315 127 ggactaatgcacaattttttaccggataatttaaaatcatctgcgtcttcctgtaagcttccttgacattacaagtatttgaatgtaatattgatagtataaatacttttattttaagaaggatact Intra-Species Hit: Count: 1 Min: 1 Max: 127 Len: 127 Subject: NC_002967_TDE1911_TDE1912|hypothetical protein:redox-sensing transcriptional repressor Rex|NEGATIVE:POSITIVE|[1929189,1929315]|127 HSP 1 e-value: 2.0E-66 bit: 252.0 Len: 127 Query Start:1 Query End:127 Subject Strand: POSITIVE Subject Start: 1 Subject End: 127 ggactaatgcacaattttttaccggataatttaaaatcatctgcgtcttcctgtaagcttccttgacattacaagtatttgaatgtaatattgatagtataaatacttttattttaagaaggatact ggactaatgcacaattttttaccggataatttaaaatcatctgcgtcttcctgtaagcttccttgacattacaagtatttgaatgtaatattgatagtataaatacttttattttaagaaggatact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGACUAAUGCACAAUUUUUUACCGGAUAAUUUAAAAUCAUCUGCGUCUUCCUGUAAGCUUCCUUGACAUUACAAGUAUUUGAAUGUAAUAUUGAUAGUAUAAAUACUUUUAUUUUAAGAAGGAUACU (((...(((((.....(((((..........))))).....)))))..))).(((..((((.((((...((.(((((((((..(((.......)))...))))))))).))..))))))))..))). (-17.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUAUCCUUCUUAAAAUAAAAGUAUUUAUACUAUCAAUAUUACAUUCAAAUACUUGUAAUGUCAAGGAAGCUUACAGGAAGACGCAGAUGAUUUUAAAUUAUCCGGUAAAAAAUUGUGCAUUAGUCC .(((..((((((........((((....))))....((((((((..........))))))))..))))))..))).....(((...((((((.....))))))..(((........)))....))). (-19.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 858 70 21 161 112 NC_002967:TDE1911|5end_hypothetical_protein_1929098..1929328_NEGATIVE 291 88 41 81 22 NC_002967:TDE0135|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_154927..155157_POSITIVE 272 66 23 117 73 NC_002967:TDE2267|5end_HRDC_domain_protein_2304464..2304694_NEGATIVE 269 62 22 123 70 NC_002967:TDE1151|5end_hypothetical_protein_1188534..1188764_NEGATIVE 268 83 48 214 177 NC_002967:TDE1225|5end_zinc_ABC_transporter,_ATP-binding_protein_1259518..1259748_NEGATIVE 259 87 43 149 119 NC_002967:TDE0701|5end_hypothetical_protein_737247..737477_NEGATIVE 252 70 22 194 145 NC_002967:TDE2283|5end_permease,_putative_2320917..2321147_NEGATIVE 248 64 22 222 179 NC_002967:TDE1863|5end_Holliday_junction_DNA_helicase_RuvA_1888579..1888809_NEGATIVE 245 62 21 53 3 NC_002967:TDE0464|5end_NifU_domain_protein_518175..518405_NEGATIVE 240 67 39 42 11 NC_002967:TDE2036|5end_ATPase,_AAA_family_2066638..2066868_NEGATIVE 240 47 11 191 145 NC_002967:TDE0398|5end_oligopeptide/dipeptide_ABC_transporter,_periplasmic_peptide-binding_protein_447773..448003_POSITIVE 238 68 22 213 161 NC_002967:TDE0314|5end_hypothetical_protein_346077..346307_POSITIVE 234 65 21 126 66 NC_002967:TDE0518|5end_hypothetical_protein_565263..565493_NEGATIVE 231 78 31 84 34 NC_002967:TDE2466|5end_hypothetical_protein_2489860..2490090_NEGATIVE 230 70 38 148 116 NC_002967:TDE1926|5end_hypothetical_protein_1942495..1942725_POSITIVE 230 66 23 104 66 NC_002967:TDE0778|5end_ribosomal_protein_L24_811487..811717_POSITIVE 229 65 39 230 208 NC_002967:TDE0190|5end_hypothetical_protein_227366..227596_NEGATIVE 228 60 11 117 71 NC_002967:TDE2296|5end_hypothetical_protein_2336337..2336567_NEGATIVE 228 65 24 106 68 NC_002967:TDE0836|5end_Na(+)-translocating_NADH-quinone_reductase,_C_subunit_856096..856326_NEGATIVE 228 69 22 105 47 NC_002967:TDE0191|5end_acetyltransferase,_GNAT_family_227806..228036_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 88 41 84 25 NC_002967:TDE0134|3end_oxidoreductase,_FAD-dependent_155010..155160_POSITIVE 269 62 22 130 77 NC_002967:TDE1152|3end_head-to-tail_joining_protein,_putative_1188527..1188677_NEGATIVE 245 68 22 139 104 NC_002967:TDE0702|3end_ABC_transporter,_ATP-binding_protein_737244..737394_NEGATIVE 240 67 39 33 2 NC_002967:TDE2037|3end_ATP:guanido_phosphotransferase_domain_protein_2066647..2066797_NEGATIVE 234 83 41 89 47 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 233 81 41 105 63 NC_002967:TDE1015|3end_hypothetical_protein_1045599..1045749_POSITIVE 231 78 31 63 13 NC_002967:TDE2467|3end_hypothetical_protein_2489881..2490031_NEGATIVE 230 66 23 94 56 NC_002967:TDE0777|3end_50S_ribosomal_protein_L14_811557..811707_POSITIVE 228 60 11 115 69 NC_002967:TDE2297|3end_TPR_domain_protein_2336339..2336489_NEGATIVE 228 65 24 109 71 NC_002967:TDE0837|3end_Na(+)-translocating_NADH-quinone_reductase,_B_subunit_856093..856243_NEGATIVE 228 69 22 94 36 NC_002967:TDE0192|3end_hypothetical_protein_227817..227967_NEGATIVE 226 89 41 60 1 NC_002967:TDE2643|3end_oxidoreductase,_FAD-dependent_2683734..2683884_POSITIVE 222 81 43 52 20 NC_002967:TDE1811|3end_hypothetical_protein_1846773..1846923_NEGATIVE 220 57 14 119 81 NC_002967:TDE2451|3end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_2480955..2481105_POSITIVE 220 62 21 73 24 NC_002967:TDE0003|3end_hypothetical_protein_4282..4432_POSITIVE 218 60 16 92 59 NC_002967:TDE0869|3end_hypothetical_protein_892662..892812_POSITIVE 215 85 42 45 10 NC_002967:TDE1600|3end_ABC_transporter,_ATP-binding/permease_protein_1650645..1650795_NEGATIVE 214 80 40 66 33 NC_002967:TDE2763|3end_flagellar_motor_switch_protein_2817737..2817887_NEGATIVE 214 70 37 109 73 NC_002967:TDE2632|3end_peptide_ABC_transporter,_ATP-binding_protein,_putative_2674424..2674574_POSITIVE 213 58 15 137 87 NC_002967:TDE2284|3end_efflux_transporter,_RND_family,_MFP_subunit_2320925..2321075_NEGATIVE