Origin IGS: tgggctccctcttctaaatagacagacatggataagcaaaaattatccgtgatagctaatttgactatatgattttttgtttgttacactctaaggtgagtcagaggacaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttgtcctctgactcaccttagagtgtaacaaacaaaaaatcatatagtcaaattagctatcacggataatttttgcttatccatgtctgtctatttagaagagggagccca Mask Tandem Repeat Region ================================================ tgggctccctcttctaaatagacagacatggataagcaaaaattatccgtgatagctaatttgactatatgattttttgtttgttacactctaaggtgagtcagaggacaa Find is-nt database================================================ Query_seq: SSA_0295:SSA_0296|SSA_0295:SSA_0296:Transcriptional regulator, LysR family, putative:Transcriptional regulator, XRE family, putative:<-<-:288992..289102 111 tgggctccctcttctaaatagacagacatggataagcaaaaattatccgtgatagctaatttgactatatgattttttgtttgttacactctaaggtgagtcagaggacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0295:SSA_0296|SSA_0295:SSA_0296:Transcriptional regulator, LysR family, putative:Transcriptional regulator, XRE family, putative:<-<-:288992..289102 111 tgggctccctcttctaaatagacagacatggataagcaaaaattatccgtgatagctaatttgactatatgattttttgtttgttacactctaaggtgagtcagaggacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0295:SSA_0296|SSA_0295:SSA_0296:Transcriptional regulator, LysR family, putative:Transcriptional regulator, XRE family, putative:<-<-:288992..289102 111 tgggctccctcttctaaatagacagacatggataagcaaaaattatccgtgatagctaatttgactatatgattttttgtttgttacactctaaggtgagtcagaggacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgggctccctcttctaaatagacagacatggataagcaaaaattatccgtgatagctaatttgactatatgattttttgtttgttacactctaaggtgagtcagaggacaa Predict ORF larger than 30AA ================================================ tgggctccctcttctaaatagacagacatggataagcaaaaattatccgtgatagctaatttgactatatgattttttgtttgttacactctaaggtgagtcagaggacaa 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================================================ tgggctccctcttctaaatagacagacatggataagcaaaaattatccgtgatagctaatttgactatatgattttttgtttgttacactctaaggtgagtcagaggacaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 45 HP_score: -2.9 Tail_Score: -3.15257 Start: 27 End: 51 Full_Region: agtcaaattagctat cacggataa tttttgc ttatccatg tctgtctatttagaa ..........................cacggataatttttgcttatccatg............................................................ Find igs database================================================ Query_seq: SSA_0295:SSA_0296|SSA_0295:SSA_0296:Transcriptional regulator, LysR family, putative:Transcriptional regulator, XRE family, putative:<-<-:288992..289102 111 tgggctccctcttctaaatagacagacatggataagcaaaaattatccgtgatagctaatttgactatatgattttttgtttgttacactctaaggtgagtcagaggacaa Intra-Species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: NC_009009_SSA_0295_SSA_0296|Transcriptional regulator, LysR family, putative:Transcriptional regulator, XRE family, putative|NEGATIVE:NEGATIVE|[288992,289102]|111 HSP 1 e-value: 7.0E-57 bit: 220.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 1 Subject End: 111 tgggctccctcttctaaatagacagacatggataagcaaaaattatccgtgatagctaatttgactatatgattttttgtttgttacactctaaggtgagtcagaggacaa tgggctccctcttctaaatagacagacatggataagcaaaaattatccgtgatagctaatttgactatatgattttttgtttgttacactctaaggtgagtcagaggacaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGGGCUCCCUCUUCUAAAUAGACAGACAUGGAUAAGCAAAAAUUAUCCGUGAUAGCUAAUUUGACUAUAUGAUUUUUUGUUUGUUACACUCUAAGGUGAGUCAGAGGACAA .......(((((....(((((((((((((((((((.......)))))))))(((((......).)))).......))))))))))..((((......)))).))))).... (-26.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUCCUCUGACUCACCUUAGAGUGUAACAAACAAAAAAUCAUAUAGUCAAAUUAGCUAUCACGGAUAAUUUUUGCUUAUCCAUGUCUGUCUAUUUAGAAGAGGGAGCCCA ...((((((.((((......))))...(((.(((.........(((((.......)))))...((((((.......)))))).))).))).........))))))...... (-19.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 886 50 1 141 92 NC_009009:SSA_0295|5end_Transcriptional_regulator,_LysR_family,_putative_288901..289131_NEGATIVE 324 50 2 49 1 NC_009009:SSA_1493|5end_hypothetical_protein_1499480..1499710_NEGATIVE 250 96 51 69 38 NC_009009:SSA_0310|5end_hypothetical_protein_305306..305536_POSITIVE 250 65 27 209 167 NC_009009:SSA_0105|5end_Uridine_kinase,_putative_106761..106991_POSITIVE 250 85 45 146 107 NC_009009:SSA_0045|5end_hypothetical_protein_50333..50563_POSITIVE 236 47 6 194 159 NC_009009:SSA_2289|5end_Cadmium_efflux_system_transcriptional_regulator_(ArsR-like),_putative_2291087..2291317_POSITIVE 236 47 6 194 159 NC_009009:SSA_2389|5end_Arsenical_resistance_operon_transcription_repressor,_putative_2032183..2032413_NEGATIVE 236 47 6 164 129 NC_009009:SSA_2387|5end_Arsenical_resistance_operon_transcription_repressor,_putative_2032213..2032443_NEGATIVE 235 37 1 54 9 NC_009009:SSA_0245|5end_hypothetical_protein_239136..239366_POSITIVE 234 83 46 65 29 NC_009009:SSA_1845|5end_Serine/threonine_protein_kinase,_putative_1840181..1840411_NEGATIVE 233 90 46 228 186 NC_009009:SSA_1527|5end_hypothetical_protein_1534587..1534817_POSITIVE 232 59 14 231 163 NC_009009:SSA_0696|5end_hypothetical_protein_679154..679384_POSITIVE 230 50 4 143 92 NC_009009:SSA_0703|5end_Citrate_synthase,_putative_688154..688384_POSITIVE 227 55 21 42 2 NC_009009:SSA_1000|5end_Galactose_operon_transcriptional_repressor,_LacI_family,_putative_1000734..1000964_NEGATIVE 227 67 25 48 8 NC_009009:SSA_0320|5end_hypothetical_protein_313406..313636_POSITIVE 227 40 6 122 92 NC_009009:SSA_0246|5end_Conserved_uncharacterized_protein_239703..239933_POSITIVE 222 108 65 214 156 NC_009009:SSA_1424|5end_Hydrolase,_putative_1434479..1434709_NEGATIVE 221 59 11 155 103 NC_009009:SSA_0735|5end_Integral_membrane_protein,_putative_717103..717333_POSITIVE 219 55 11 63 16 NC_009009:SSA_1725|5end_Branched-chain_amino_acid_ABC_transporter,_ATP-binding_protein,_putative_1711703..1711933_NEGATIVE 218 58 14 63 2 NC_009009:SSA_2039|5end_Aminoacid_specific_permease,_putative_2044455..2044685_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 250 96 51 76 45 NC_009009:SSA_0309|3end_Glyoxalase/Bleomycin_resistance_protein/dioxygenase_domain,_putative_305393..305543_POSITIVE 237 67 23 137 97 NC_009009:SSA_0253|3end_CAAX_amino_terminal_protease_family_protein,_putative_246983..247133_POSITIVE 234 83 46 68 32 NC_009009:SSA_1846|3end_Phosphoprotein_phosphatase,_putative_1840178..1840328_NEGATIVE 232 57 22 37 1 NC_009009:SSA_0486|3end_Uroporphyrinogen-III_synthase,_putative_487442..487592_POSITIVE 230 50 4 140 89 NC_009009:SSA_0702|3end_Aconitase_A,_putative_688231..688381_POSITIVE 227 100 54 62 11 NC_009009:SSA_0649|3end_Ribosomal_small_subunit_pseudouridine_synthase_A,_putative_631820..631970_NEGATIVE 227 67 25 58 18 NC_009009:SSA_0319|3end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_313496..313646_POSITIVE 219 55 11 63 16 NC_009009:SSA_1726|3end_ABC_transporter_ATP-binding_protein-branched_chain_amino_acid_transport,_putative_1711703..1711853_NEGATIVE 218 58 11 70 24 NC_009009:SSA_0187|3end_Competence_protein_ComYD,_putative_190852..191002_POSITIVE 216 38 3 69 22 NC_009009:SSA_2273|3end_hypothetical_protein_2272897..2273047_NEGATIVE 211 90 42 92 48 NC_009009:SSA_0991|3end_Deoxyribonuclease,_putative_992581..992731_NEGATIVE 210 102 61 142 100 NC_009009:SSA_0197|3end_Dihydropteroate_synthase,_putative_196979..197129_POSITIVE 209 49 1 70 18 NC_009009:SSA_1745|3end_General_stress_response_protein_CsbD,_putative_1731997..1732147_NEGATIVE 208 56 20 42 4 NC_009009:SSA_0495|3end_ABC-type_oligopeptide/nickel_transport_system,_ATPase_component,_putative_496036..496186_POSITIVE 208 41 1 58 9 NC_009009:SSA_0293|3end_hypothetical_protein_287356..287506_NEGATIVE 207 108 70 36 3 NC_009009:SSA_0822|3end_Large_conductance_mechano-sensitive_ion_channel,_putative_801589..801739_NEGATIVE 206 63 23 111 74 NC_009009:SSA_1451|3end_Exonuclease_RexA,_putative_1452744..1452894_NEGATIVE 202 49 1 73 19 NC_009009:SSA_2275|3end_hypothetical_protein_2275225..2275375_NEGATIVE 202 50 1 62 6 NC_009009:SSA_2072|3end_Phosphatidate_cytidylyltransferase,_putative_2074800..2074950_NEGATIVE 200 50 2 138 94 NC_009009:SSA_1989|3end_ABC-type_transport_system_(uncharacterized),_ATPase_component,_putative_1984190..1984340_NEGATIVE