Origin IGS: tctattcctctcaaaaattcatttctaccattgtaccctaaaaggaaggggatttcaaatattagtgacaagacagtttaagaggaagctaaccagaaagtcgcttgcttaggggcatcaatgccataagtatactcaaagtattttggaaccagatcttaagaaagctcgtaaagcatcacaattagtaaacgttaattcgaaagaattactatattttaaaagagcacattttcaaaggattttttcttttgccttcaattcctaattaatcaatgaatttaatactaggtctcgaaaagaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttcttttcgagacctagtattaaattcattgattaattaggaattgaaggcaaaagaaaaaatcctttgaaaatgtgctcttttaaaatatagtaattctttcgaattaacgtttactaattgtgatgctttacgagctttcttaagatctggttccaaaatactttgagtatacttatggcattgatgcccctaagcaagcgactttctggttagcttcctcttaaactgtcttgtcactaatatttgaaatccccttccttttagggtacaatggtagaaatgaatttttgagaggaataga Mask Tandem Repeat Region ================================================ tctattcctctcaaaaattcatttctaccattgtaccctaaaaggaaggggatttcaaatattagtgacaagacagtttaagaggaagctaaccagaaagtcgcttgcttaggggcatcaatgccataagtatactcaaagtattttggaaccagatcttaagaaagctcgtaaagcatcacaattagtaaacgttaattcgaaagaattactatattttaaaagagcacattttcaaaggattttttcttttgccttcaattcctaattaatcaatgaatttaatactaggtctcgaaaagaa Find is-nt database================================================ Query_seq: SMT_502:SMT_503|SMT_502:SMT_503:peptidyl-prolyl cis-trans isomerase, cyclophilin-type:K07729 putative transcriptional regulator:<-<-:435766..436069 304 tctattcctctcaaaaattcatttctaccattgtaccctaaaaggaaggggatttcaaatattagtgacaagacagtttaagaggaagctaaccagaaagtcgcttgcttaggggcatcaatgccataagtatactcaaagtattttggaaccagatcttaagaaagctcgtaaagcatcacaattagtaaacgttaattcgaaagaattactatattttaaaagagcacattttcaaaggattttttcttttgccttcaattcctaattaatcaatgaatttaatactaggtctcgaaaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_502:SMT_503|SMT_502:SMT_503:peptidyl-prolyl cis-trans isomerase, cyclophilin-type:K07729 putative transcriptional regulator:<-<-:435766..436069 304 tctattcctctcaaaaattcatttctaccattgtaccctaaaaggaaggggatttcaaatattagtgacaagacagtttaagaggaagctaaccagaaagtcgcttgcttaggggcatcaatgccataagtatactcaaagtattttggaaccagatcttaagaaagctcgtaaagcatcacaattagtaaacgttaattcgaaagaattactatattttaaaagagcacattttcaaaggattttttcttttgccttcaattcctaattaatcaatgaatttaatactaggtctcgaaaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_502:SMT_503|SMT_502:SMT_503:peptidyl-prolyl cis-trans isomerase, cyclophilin-type:K07729 putative transcriptional regulator:<-<-:435766..436069 304 tctattcctctcaaaaattcatttctaccattgtaccctaaaaggaaggggatttcaaatattagtgacaagacagtttaagaggaagctaaccagaaagtcgcttgcttaggggcatcaatgccataagtatactcaaagtattttggaaccagatcttaagaaagctcgtaaagcatcacaattagtaaacgttaattcgaaagaattactatattttaaaagagcacattttcaaaggattttttcttttgccttcaattcctaattaatcaatgaatttaatactaggtctcgaaaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctattcctctcaaaaattcatttctaccattgtaccctaaaaggaaggggatttcaaatattagtgacaagacagtttaagaggaagctaaccagaaagtcgcttgcttaggggcatcaatgccataagtatactcaaagtattttggaaccagatcttaagaaagctcgtaaagcatcacaattagtaaacgttaattcgaaagaattactatattttaaaagagcacattttcaaaggattttttcttttgccttcaattcctaattaatcaatgaatttaatactaggtctcgaaaagaa Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 17 End: 109 ................ M H F Y H C T L K G R G F Q I L V T R Q F K R K L T R K S L A ................................................................................................................................................................................................... Protein_Len: 41 Strand: + Start: 143 End: 265 .............................................................................................................................................. M L E P D L K K A R K A S Q L V N V N S K E L L Y F K R A H F Q R I F S F A F N S ....................................... tctattcctctcaaaaattcatttctaccattgtaccctaaaaggaaggggatttcaaatattagtgacaagacagtttaagaggaagctaaccagaaagtcgcttgcttaggggcatcaatgccataagtatactcaaagtattttggaaccagatcttaagaaagctcgtaaagcatcacaattagtaaacgttaattcgaaagaattactatattttaaaagagcacattttcaaaggattttttcttttgccttcaattcctaattaatcaatgaatttaatactaggtctcgaaaagaa 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: 88 Start: 30 End: 59 .............................TTTGAAATCCCCTTCCTTTTAGGGTACAAT..................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tctattcctctcaaaaattcatttctaccattgtaccctaaaaggaaggggatttcaaatattagtgacaagacagtttaagaggaagctaaccagaaagtcgcttgcttaggggcatcaatgccataagtatactcaaagtattttggaaccagatcttaagaaagctcgtaaagcatcacaattagtaaacgttaattcgaaagaattactatattttaaaagagcacattttcaaaggattttttcttttgccttcaattcctaattaatcaatgaatttaatactaggtctcgaaaagaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_502:SMT_503|SMT_502:SMT_503:peptidyl-prolyl cis-trans isomerase, cyclophilin-type:K07729 putative transcriptional regulator:<-<-:435766..436069 304 tctattcctctcaaaaattcatttctaccattgtaccctaaaaggaaggggatttcaaatattagtgacaagacagtttaagaggaagctaaccagaaagtcgcttgcttaggggcatcaatgccataagtatactcaaagtattttggaaccagatcttaagaaagctcgtaaagcatcacaattagtaaacgttaattcgaaagaattactatattttaaaagagcacattttcaaaggattttttcttttgccttcaattcctaattaatcaatgaatttaatactaggtctcgaaaagaa Intra-Species Hit: Count: 2 Min: 1 Max: 304 Len: 304 Subject: smit_SMT_505_SMT_506|peptidyl-prolyl cis-trans isomerase, cyclophilin-type:K07729 putative transcriptional regulator|NEGATIVE:NEGATIVE|[437197,437500]|304 HSP 1 e-value: 1.0E-171 bit: 603.0 Len: 304 Query Start:1 Query End:304 Subject Strand: POSITIVE Subject Start: 1 Subject End: 304 tctattcctctcaaaaattcatttctaccattgtaccctaaaaggaaggggatttcaaatattagtgacaagacagtttaagaggaagctaaccagaaagtcgcttgcttaggggcatcaatgccataagtatactcaaagtattttggaaccagatcttaagaaagctcgtaaagcatcacaattagtaaacgttaattcgaaagaattactatattttaaaagagcacattttcaaaggattttttcttttgccttcaattcctaattaatcaatgaatttaatactaggtctcgaaaagaa tctattcctctcaaaaattcatttctaccattgtaccctaaaaggaaggggatttcaaatattagtgacaagacagtttaagaggaagctaaccagaaagtcgcttgcttaggggcatcaatgccataagtatactcaaagtattttggaaccagatcttaagaaagctcgtaaagcatcacaattagtaaacgttaattcgaaagaattactatattttaaaagagcacattttcaaaggattttttcttttgccttcaattcctaattaatcaatgaatttaatactaggtctcgaaaagaa Subject: smit_SMT_502_SMT_503|peptidyl-prolyl cis-trans isomerase, cyclophilin-type:K07729 putative transcriptional regulator|NEGATIVE:NEGATIVE|[435766,436069]|304 HSP 1 e-value: 1.0E-171 bit: 603.0 Len: 304 Query Start:1 Query End:304 Subject Strand: POSITIVE Subject Start: 1 Subject End: 304 tctattcctctcaaaaattcatttctaccattgtaccctaaaaggaaggggatttcaaatattagtgacaagacagtttaagaggaagctaaccagaaagtcgcttgcttaggggcatcaatgccataagtatactcaaagtattttggaaccagatcttaagaaagctcgtaaagcatcacaattagtaaacgttaattcgaaagaattactatattttaaaagagcacattttcaaaggattttttcttttgccttcaattcctaattaatcaatgaatttaatactaggtctcgaaaagaa tctattcctctcaaaaattcatttctaccattgtaccctaaaaggaaggggatttcaaatattagtgacaagacagtttaagaggaagctaaccagaaagtcgcttgcttaggggcatcaatgccataagtatactcaaagtattttggaaccagatcttaagaaagctcgtaaagcatcacaattagtaaacgttaattcgaaagaattactatattttaaaagagcacattttcaaaggattttttcttttgccttcaattcctaattaatcaatgaatttaatactaggtctcgaaaagaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUAUUCCUCUCAAAAAUUCAUUUCUACCAUUGUACCCUAAAAGGAAGGGGAUUUCAAAUAUUAGUGACAAGACAGUUUAAGAGGAAGCUAACCAGAAAGUCGCUUGCUUAGGGGCAUCAAUGCCAUAAGUAUACUCAAAGUAUUUUGGAACCAGAUCUUAAGAAAGCUCGUAAAGCAUCACAAUUAGUAAACGUUAAUUCGAAAGAAUUACUAUAUUUUAAAAGAGCACAUUUUCAAAGGAUUUUUUCUUUUGCCUUCAAUUCCUAAUUAAUCAAUGAAUUUAAUACUAGGUCUCGAAAAGAA ((....(((.....(((((((((............((((........)))).........(((((.((...((..((..(((((((......(((((((((....((((((..((((....)))).)))))).))).......)))))).....((((((..((((((((.(((((....((.....))......((((((....)))))).....)))))...))))....))))..)))))))))))))..))..))...))))))).....)))))))))......)))....))...... (-54.01) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUUUUCGAGACCUAGUAUUAAAUUCAUUGAUUAAUUAGGAAUUGAAGGCAAAAGAAAAAAUCCUUUGAAAAUGUGCUCUUUUAAAAUAUAGUAAUUCUUUCGAAUUAACGUUUACUAAUUGUGAUGCUUUACGAGCUUUCUUAAGAUCUGGUUCCAAAAUACUUUGAGUAUACUUAUGGCAUUGAUGCCCCUAAGCAAGCGACUUUCUGGUUAGCUUCCUCUUAAACUGUCUUGUCACUAAUAUUUGAAAUCCCCUUCCUUUUAGGGUACAAUGGUAGAAAUGAAUUUUUGAGAGGAAUAGA ((((((((((((.....((((....((((((.....((((((.(..((((.............))))..)......((((.............((((((....))))))..((((((.....)))).)).....))))..))))))....((((..(((.(((.((((((....((((.((((....))))..)))).((((((((....)))).))))...)))))).))).)))..))))............((((.......))))..))))))....))))...)))))))))))).... (-57.02) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 978 130 81 221 172 smit:SMT_505|5end_peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type_437106..437336_NEGATIVE 978 130 81 221 172 smit:SMT_502|5end_peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type_435675..435905_NEGATIVE 307 114 71 215 169 smit:SMT_1062|5end_hypothetical_protein_1000281..1000511_POSITIVE 303 128 81 111 56 smit:SMT_826|5end_hypothetical_protein_750022..750252_NEGATIVE 298 110 64 157 112 smit:SMT_1375|5end_putative_glucose-inhibited_division_protein_1354438..1354668_NEGATIVE 287 115 71 204 141 smit:SMT_1714|5end_hypothetical_membrane_spanning_protein_1701356..1701586_POSITIVE 279 159 111 53 9 smit:SMT_2134|5end_hypothetical_protein_2014700..2014930_NEGATIVE 279 159 111 53 9 smit:SMT_873|5end_hypothetical_protein_821311..821541_NEGATIVE 276 123 88 230 186 smit:SMT_1888|5end_K02026_multiple_sugar_transport_system_permease_protein_1842088..1842318_POSITIVE 275 126 81 54 9 smit:SMT_155|5end_hypothetical_protein_102704..102934_NEGATIVE 272 298 258 55 15 smit:SMT_1258|5end_acetolactate_synthase_large_subunit_1224866..1225096_NEGATIVE 270 117 71 159 107 smit:SMT_1696|5end_hypothetical_protein_1678182..1678412_POSITIVE 269 148 102 178 108 smit:SMT_1151|5end_histidyl-tRNA_synthetase_1096168..1096398_NEGATIVE 266 146 105 206 162 smit:SMT_1329|5end_GTP-binding_protein_CgtA_1305788..1306018_NEGATIVE 266 127 83 83 34 smit:SMT_400|5end_hypothetical_protein_329090..329320_POSITIVE 265 126 89 218 184 smit:SMT_832|5end_hypothetical_protein_775104..775334_NEGATIVE 265 157 111 165 125 smit:SMT_608|5end_laminin-binding_surface_protein_520757..520987_POSITIVE 260 127 88 91 45 smit:SMT_1891|5end_putative_dihydrolipoamide_S-acetyltransferase_1844373..1844603_POSITIVE 260 127 88 91 45 smit:SMT_1402|5end_pyruvate_dehydrogenase_E2_component_(dihydrolipoamide_acetyltransferase)_1378115..1378345_POSITIVE 260 50 1 150 100 smit:SMT_659|5end_hypothetical_protein_570545..570775_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 740 300 251 86 37 smit:SMT_506|3end_K07729_putative_transcriptional_regulator_437411..437561_NEGATIVE 284 124 83 59 16 smit:SMT_1477|3end_K02077_zinc/manganese_transport_system_substrate-binding_protein_1459447..1459597_NEGATIVE 272 116 75 83 38 smit:SMT_1814|3end_amino_acid_transporter_1788640..1788790_POSITIVE 267 124 83 58 15 smit:SMT_1140|3end_glycogen_phosphorylase_1081316..1081466_NEGATIVE 266 109 64 63 3 smit:SMT_1369|3end_alanine_dehydrogenase_1349472..1349622_POSITIVE 266 146 105 142 98 smit:SMT_1330|3end_hypothetical_protein_1305852..1306002_NEGATIVE 266 127 83 69 20 smit:SMT_399|3end_cytochrome_c-type_biogenesis_protein_CcdA_329156..329306_POSITIVE 265 126 89 139 105 smit:SMT_833|3end_hypothetical_protein_predicted_by_Glimmer/Critica_775183..775333_NEGATIVE 265 157 111 144 104 smit:SMT_607|3end_K03294_basic_amino_acid/polyamine_antiporter,_APA_family_520816..520966_POSITIVE 260 124 82 64 6 smit:SMT_1488|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1468982..1469132_POSITIVE 258 136 92 57 4 smit:SMT_1588|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1578425..1578575_POSITIVE 251 126 83 143 93 smit:SMT_1981|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1912868..1913018_POSITIVE 251 39 1 128 81 smit:SMT_977|3end_conserved_hypothetical_protein,_Rrf2_family_protein_925252..925402_NEGATIVE 251 148 102 64 9 smit:SMT_366|3end_hypothetical_protein_302398..302548_POSITIVE 244 138 92 73 13 smit:SMT_2037|3end_lysine_decarboxylase_1947880..1948030_NEGATIVE 244 138 92 73 13 smit:SMT_1418|3end_lysine_decarboxylase_1401687..1401837_NEGATIVE 242 149 104 45 6 smit:SMT_651|3end_DNA_ligase_559986..560136_NEGATIVE 241 126 82 68 9 smit:SMT_1786|3end_phenylalanyl-tRNA_synthetase_beta_chain_1763235..1763385_NEGATIVE 241 129 87 126 82 smit:SMT_1331|3end_hypothetical_protein_1306045..1306195_NEGATIVE 241 128 81 82 34 smit:SMT_753|3end_chorismate_synthase_656801..656951_NEGATIVE