Origin IGS: ttctgtaaatcctttgattgcttctnnnnnttaattaattaannnnngcgagtcgctcttgtttgtgagtctcccagcatatcctgactaaaaaagttagagattctgcttccaaggtaatttggatatcaatatgaagatcaatacggtatgcatycccatat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atatgggratgcataccgtattgatcttcatattgatatccaaattaccttggaagcagaatctctaacttttttagtcaggatatgctgggagactcacaaacaagagcgactcgcnnnnnttaattaattaannnnnagaagcaatcaaaggatttacagaa Mask Tandem Repeat Region ================================================ ttctgtaaatcctttgattgcttctnnnnnttaattaattaannnnngcgagtcgctcttgtttgtgagtctcccagcatatcctgactaaaaaagttagagattctgcttccaaggtaatttggatatcaatatgaagatcaatacggtatgcatycccatat Find is-nt database================================================ Query_seq: SMT_2117:SMT_2118|SMT_2117:SMT_2118:transcription-repair coupling factor:putative two-component sensor histidine kinase:<-<-:2004651..2004814 164 ttctgtaaatcctttgattgcttctnnnnnttaattaattaannnnngcgagtcgctcttgtttgtgagtctcccagcatatcctgactaaaaaagttagagattctgcttccaaggtaatttggatatcaatatgaagatcaatacggtatgcatycccatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_2117:SMT_2118|SMT_2117:SMT_2118:transcription-repair coupling factor:putative two-component sensor histidine kinase:<-<-:2004651..2004814 164 ttctgtaaatcctttgattgcttctnnnnnttaattaattaannnnngcgagtcgctcttgtttgtgagtctcccagcatatcctgactaaaaaagttagagattctgcttccaaggtaatttggatatcaatatgaagatcaatacggtatgcatycccatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_2117:SMT_2118|SMT_2117:SMT_2118:transcription-repair coupling factor:putative two-component sensor histidine kinase:<-<-:2004651..2004814 164 ttctgtaaatcctttgattgcttctnnnnnttaattaattaannnnngcgagtcgctcttgtttgtgagtctcccagcatatcctgactaaaaaagttagagattctgcttccaaggtaatttggatatcaatatgaagatcaatacggtatgcatycccatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttctgtaaatcctttgattgcttctnnnnnttaattaattaannnnngcgagtcgctcttgtttgtgagtctcccagcatatcctgactaaaaaagttagagattctgcttccaaggtaatttggatatcaatatgaagatcaatacggtatgcatycccatat Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: - Start: 38 End: 145 ..................................... N X X A L R E Q K H T E W C I R V L F T L S E A E L T I Q I D I H L D M ................... ttctgtaaatcctttgattgcttctnnnnnttaattaattaannnnngcgagtcgctcttgtttgtgagtctcccagcatatcctgactaaaaaagttagagattctgcttccaaggtaatttggatatcaatatgaagatcaatacggtatgcatycccatat 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================================================ ttctgtaaatcctttgattgcttctnnnnnttaattaattaannnnngcgagtcgctcttgtttgtgagtctcccagcatatcctgactaaaaaagttagagattctgcttccaaggtaatttggatatcaatatgaagatcaatacggtatgcatycccatat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_2117:SMT_2118|SMT_2117:SMT_2118:transcription-repair coupling factor:putative two-component sensor histidine kinase:<-<-:2004651..2004814 164 ttctgtaaatcctttgattgcttctnnnnnttaattaattaannnnngcgagtcgctcttgtttgtgagtctcccagcatatcctgactaaaaaagttagagattctgcttccaaggtaatttggatatcaatatgaagatcaatacggtatgcatycccatat Intra-Species Hit: Count: 1 Min: 1 Max: 164 Len: 164 Subject: smit_SMT_2117_SMT_2118|transcription-repair coupling factor:putative two-component sensor histidine kinase|NEGATIVE:NEGATIVE|[2004651,2004814]|164 HSP 1 e-value: 1.0E-69 bit: 263.0 Len: 164 Query Start:1 Query End:164 Subject Strand: POSITIVE Subject Start: 1 Subject End: 164 ttctgtaaatcctttgattgcttctnnnnnttaattaattaannnnngcgagtcgctcttgtttgtgagtctcccagcatatcctgactaaaaaagttagagattctgcttccaaggtaatttggatatcaatatgaagatcaatacggtatgcatycccatat ttctgtaaatcctttgattgcttctnnnnnttaattaattaannnnngcgagtcgctcttgtttgtgagtctcccagcatatcctgactaaaaaagttagagattctgcttccaaggtaatttggatatcaatatgaagatcaatacggtatgcatycccatat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUGUAAAUCCUUUGAUUGCUUCUNNNNNUUAAUUAAUUAANNNNNGCGAGUCGCUCUUGUUUGUGAGUCUCCCAGCAUAUCCUGACUAAAAAAGUUAGAGAUUCUGCUUCCAAGGUAAUUUGGAUAUCAAUAUGAAGAUCAAUACGGUAUGCAUYCCCAUAU ...((((.(((..(((((..((((.........................((.((((........)))).))....((((.(((((((((.....)))))).)))..))))((((((....)))))).........)))))))))...))).))))......... (-32.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUGGGRAUGCAUACCGUAUUGAUCUUCAUAUUGAUAUCCAAAUUACCUUGGAAGCAGAAUCUCUAACUUUUUUAGUCAGGAUAUGCUGGGAGACUCACAAACAAGAGCGACUCGCNNNNNUUAAUUAAUUAANNNNNAGAAGCAAUCAAAGGAUUUACAGAA ((((((.........)))))).((((((....(((((.(((((......))))).((...(((.((.(((.....))).)))))..((.((..(.(((........))))..)).))..........................)).)))))))))))....... (-24.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 899 100 51 191 142 smit:SMT_2117|5end_transcription-repair_coupling_factor_2004560..2004790_NEGATIVE 305 79 31 230 174 smit:SMT_1993|5end_hypothetical_protein_1919800..1920030_NEGATIVE 294 89 48 179 133 smit:SMT_367|5end_hypothetical_protein_302318..302548_POSITIVE 271 104 61 46 10 smit:SMT_1049|5end_hypothetical_protein_988438..988668_POSITIVE 262 90 48 101 60 smit:SMT_1891|5end_putative_dihydrolipoamide_S-acetyltransferase_1844373..1844603_POSITIVE 262 90 48 101 60 smit:SMT_1402|5end_pyruvate_dehydrogenase_E2_component_(dihydrolipoamide_acetyltransferase)_1378115..1378345_POSITIVE 258 91 52 113 60 smit:SMT_2015|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1932655..1932885_POSITIVE 256 131 95 124 83 smit:SMT_1012|5end_xanthine_permease_949154..949384_POSITIVE 250 76 50 104 78 smit:SMT_138|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_89262..89492_POSITIVE 247 89 48 97 58 smit:SMT_1977|5end_endopeptidase_O_1907832..1908062_POSITIVE 244 150 104 49 14 smit:SMT_307|5end_K02078_acyl_carrier_protein_249187..249417_POSITIVE 241 89 52 185 140 smit:SMT_1873|5end_K02006_cobalt_transport_system_ATP-binding_protein_1831936..1832166_POSITIVE 241 139 95 58 17 smit:SMT_1411|5end_ATP-dependent_nuclease_subunit_B_1395478..1395708_NEGATIVE 240 87 51 209 183 smit:SMT_794|5end_hypothetical_protein_703487..703717_NEGATIVE 237 113 71 139 82 smit:SMT_1437|5end_ADP-ribosylglycohydrolase_1422219..1422449_NEGATIVE 237 83 48 215 176 smit:SMT_514|5end_tRNA_(guanine-N(1)-)-methyltransferase_441377..441607_POSITIVE 236 114 74 57 15 smit:SMT_1555|5end_hypothetical_protein_1541014..1541244_NEGATIVE 236 90 48 205 153 smit:SMT_382|5end_valyl-tRNA_synthetase_317706..317936_POSITIVE 236 139 105 220 183 smit:SMT_177|5end_K02878_large_subunit_ribosomal_protein_L16_118738..118968_POSITIVE 233 89 48 223 172 smit:SMT_1060|5end_K03977_GTP-binding_protein_998106..998336_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 315 80 49 144 110 smit:SMT_1514|3end_methylenetetrahydrofolate_dehydrogenase_(NADP+)_/_methenyltetrahydrofolate_cyclohydrolase_1495720..1495870_NEGATIVE 271 104 61 49 13 smit:SMT_1048|3end_K06518_holin-like_protein_988521..988671_POSITIVE 258 91 52 105 52 smit:SMT_2014|3end_tryptophan_synthase_beta_chain_1932727..1932877_POSITIVE 256 78 53 81 55 smit:SMT_1069|3end_acetyl_xylan_esterase,_putative_1009595..1009745_POSITIVE 256 131 95 124 83 smit:SMT_1011|3end_xanthine_phosphoribosyltransferase_949234..949384_POSITIVE 251 108 65 49 11 smit:SMT_1695|3end_ribulose-phosphate_3-epimerase_1678299..1678449_POSITIVE 247 85 48 146 105 smit:SMT_937|3end_dipeptidase_890741..890891_POSITIVE 246 89 53 140 101 smit:SMT_365|3end_hypothetical_protein_301747..301897_POSITIVE 243 119 79 74 27 smit:SMT_710|3end_hypothetical_protein_predicted_by_Glimmer/Critica_619270..619420_NEGATIVE 238 79 48 151 116 smit:SMT_1681|3end_D-alanine-activating_enzyme_1665052..1665202_POSITIVE 237 113 71 98 41 smit:SMT_1438|3end_hypothetical_protein_1422260..1422410_NEGATIVE 230 80 48 135 96 smit:SMT_1015|3end_galactose_operon_repressor_953019..953169_POSITIVE 229 100 53 120 69 smit:SMT_120|3end_hypothetical_protein_72943..73093_POSITIVE 227 80 48 48 20 smit:SMT_1480|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1462266..1462416_POSITIVE 227 74 48 67 34 smit:SMT_1071|3end_hypothetical_protein_1010386..1010536_POSITIVE 227 78 31 138 87 smit:SMT_986|3end_threonyl-tRNA_synthetase_931684..931834_POSITIVE 226 79 50 151 112 smit:SMT_1836|3end_cytidine/deoxycytidylate_deaminase_family_protein_1804100..1804250_NEGATIVE 226 99 51 74 20 smit:SMT_855|3end_dihydrofolate_reductase_799492..799642_NEGATIVE 224 87 50 69 26 smit:SMT_1678|3end_inorganic_pyrophosphatase_1662991..1663141_POSITIVE 224 149 103 146 93 smit:SMT_507|3end_hypothetical_protein_437638..437788_NEGATIVE