Origin IGS: agaataaatccttataaatataaaatatatagaaggcgtaagaatatcagtcttttaaaaaacagtcaatagccggacttttacattctttcccaaataggct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agcctatttgggaaagaatgtaaaagtccggctattgactgttttttaaaagactgatattcttacgccttctatatattttatatttataaggatttattct Mask Tandem Repeat Region ================================================ agaataaatccttataaatataaaatatatagaaggcgtaagaatatcagtcttttaaaaaacagtcaatagccggacttttacattctttcccaaataggct Find is-nt database================================================ Query_seq: TDE2287:TDE2288|TDE2287:TDE2288:peptidyl-prolyl cis-trans isomerase, FKBP-type:hypothetical protein:<-<-:2325149..2325251 103 agaataaatccttataaatataaaatatatagaaggcgtaagaatatcagtcttttaaaaaacagtcaatagccggacttttacattctttcccaaataggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2287:TDE2288|TDE2287:TDE2288:peptidyl-prolyl cis-trans isomerase, FKBP-type:hypothetical protein:<-<-:2325149..2325251 103 agaataaatccttataaatataaaatatatagaaggcgtaagaatatcagtcttttaaaaaacagtcaatagccggacttttacattctttcccaaataggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2287:TDE2288|TDE2287:TDE2288:peptidyl-prolyl cis-trans isomerase, FKBP-type:hypothetical protein:<-<-:2325149..2325251 103 agaataaatccttataaatataaaatatatagaaggcgtaagaatatcagtcttttaaaaaacagtcaatagccggacttttacattctttcccaaataggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agaataaatccttataaatataaaatatatagaaggcgtaagaatatcagtcttttaaaaaacagtcaatagccggacttttacattctttcccaaataggct Predict ORF larger than 30AA ================================================ agaataaatccttataaatataaaatatatagaaggcgtaagaatatcagtcttttaaaaaacagtcaatagccggacttttacattctttcccaaataggct 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: 82 Start: 41 End: 70 ........................................ATTGACTGTTTTTTAAAAGACTGATATTCT................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agaataaatccttataaatataaaatatatagaaggcgtaagaatatcagtcttttaaaaaacagtcaatagccggacttttacattctttcccaaataggct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2287:TDE2288|TDE2287:TDE2288:peptidyl-prolyl cis-trans isomerase, FKBP-type:hypothetical protein:<-<-:2325149..2325251 103 agaataaatccttataaatataaaatatatagaaggcgtaagaatatcagtcttttaaaaaacagtcaatagccggacttttacattctttcccaaataggct Intra-Species Hit: Count: 1 Min: 1 Max: 103 Len: 103 Subject: NC_002967_TDE2287_TDE2288|peptidyl-prolyl cis-trans isomerase, FKBP-type:hypothetical protein|NEGATIVE:NEGATIVE|[2325149,2325251]|103 HSP 1 e-value: 4.0E-52 bit: 204.0 Len: 103 Query Start:1 Query End:103 Subject Strand: POSITIVE Subject Start: 1 Subject End: 103 agaataaatccttataaatataaaatatatagaaggcgtaagaatatcagtcttttaaaaaacagtcaatagccggacttttacattctttcccaaataggct agaataaatccttataaatataaaatatatagaaggcgtaagaatatcagtcttttaaaaaacagtcaatagccggacttttacattctttcccaaataggct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAUAAAUCCUUAUAAAUAUAAAAUAUAUAGAAGGCGUAAGAAUAUCAGUCUUUUAAAAAACAGUCAAUAGCCGGACUUUUACAUUCUUUCCCAAAUAGGCU (((((........................((((((((............))))))))......((((........)))).....))))).............. (-10.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCCUAUUUGGGAAAGAAUGUAAAAGUCCGGCUAUUGACUGUUUUUUAAAAGACUGAUAUUCUUACGCCUUCUAUAUAUUUUAUAUUUAUAAGGAUUUAUUCU ..(((....(((.((((((((...((((((((....).)))..........)))).)))))))).).))...((((.....))))......)))......... (-14.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 832 80 31 171 122 NC_002967:TDE2287|5end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_2325058..2325288_NEGATIVE 260 80 38 142 105 NC_002967:TDE0961|5end_DnaJ_domain_protein_983519..983749_POSITIVE 244 95 51 199 167 NC_002967:TDE2062|5end_hypothetical_protein_2088344..2088574_NEGATIVE 236 67 26 150 109 NC_002967:TDE2219|5end_hypothetical_protein_2260646..2260876_NEGATIVE 235 80 31 189 135 NC_002967:TDE2715|5end_hypothetical_protein_2772668..2772898_POSITIVE 233 76 31 186 137 NC_002967:TDE2623|5end_hypothetical_protein_2664324..2664554_NEGATIVE 227 79 33 100 60 NC_002967:TDE1110|5end_lipoprotein,_putative_1144272..1144502_POSITIVE 217 77 31 189 138 NC_002967:TDE2528|5end_hypothetical_protein_2556912..2557142_NEGATIVE 213 94 57 207 156 NC_002967:TDE0046|5end_formiminotransferase-cyclodeaminase_family_protein_55849..56079_NEGATIVE 211 80 31 61 12 NC_002967:TDE0180|5end_hypothetical_protein_213018..213248_NEGATIVE 211 80 31 198 149 NC_002967:TDE0179|5end_hypothetical_protein_212881..213111_NEGATIVE 209 77 31 50 2 NC_002967:TDE2684|5end_hypothetical_protein_2724848..2725078_NEGATIVE 208 85 43 108 72 NC_002967:TDE2662|5end_lipoprotein,_putative_2698650..2698880_NEGATIVE 207 55 11 185 141 NC_002967:TDE1041|5end_polyribonucleotide_nucleotidyltransferase_1068324..1068554_POSITIVE 206 80 35 212 158 NC_002967:TDE2616|5end_cyclic_nucleotide-binding_protein_2658339..2658569_NEGATIVE 206 60 12 80 22 NC_002967:TDE0959|5end_hypothetical_protein_981935..982165_POSITIVE 206 95 51 186 134 NC_002967:TDE0134|5end_oxidoreductase,_FAD-dependent_153404..153634_POSITIVE 205 82 49 217 185 NC_002967:TDE2669|5end_CDP-alcohol_phosphatidyltransferase_family_protein_2706943..2707173_NEGATIVE 204 80 32 72 13 NC_002967:TDE0872|5end_recA_protein_894841..895071_POSITIVE 203 100 62 66 25 NC_002967:TDE0064|5end_diphosphate--fructose-6-phosphate_1-phosphotransferase_72651..72881_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 271 80 31 128 73 NC_002967:TDE0575|3end_aspartyl/glutamyl-tRNA_amidotransferase_subunit_B_606252..606402_NEGATIVE 260 80 38 138 101 NC_002967:TDE0960|3end_neuB_family_protein_983595..983745_POSITIVE 244 95 51 113 81 NC_002967:TDE2063|3end_ferrous_iron_transport_protein_B_2088430..2088580_NEGATIVE 227 79 33 77 37 NC_002967:TDE1109|3end_decarboxylase,_pyridoxal-dependent_family_1144329..1144479_POSITIVE 217 77 31 123 72 NC_002967:TDE2529|3end_hypothetical_protein_2556978..2557128_NEGATIVE 213 94 57 136 85 NC_002967:TDE0047|3end_imidazolonepropionase_55920..56070_NEGATIVE 211 80 31 92 43 NC_002967:TDE0181|3end_methyl-accepting_chemotaxis_protein_212987..213137_NEGATIVE 208 85 43 142 106 NC_002967:TDE2663|3end_isoleucyl-tRNA_synthetase_2698616..2698766_NEGATIVE 207 55 11 69 25 NC_002967:TDE1040|3end_ribosomal_protein_S15_1068288..1068438_POSITIVE 206 60 12 96 38 NC_002967:TDE0958|3end_patatin_family_protein_982031..982181_POSITIVE 198 75 31 77 34 NC_002967:TDE1046|3end_hypothetical_protein_1074076..1074226_POSITIVE 196 73 32 67 31 NC_002967:TDE1548|3end_conserved_hypothetical_protein_TIGR00103_1592202..1592352_POSITIVE 195 77 40 111 72 NC_002967:TDE1743|3end_chromate_transport_protein_1797940..1798090_NEGATIVE 194 80 33 67 8 NC_002967:TDE0341|3end_ribonucleotide-diphosphate_reductase_alpha_subunit_379589..379739_NEGATIVE 193 78 37 103 65 NC_002967:TDE2517|3end_DNA_repair_protein_RadA_2542454..2542604_NEGATIVE 193 79 45 81 42 NC_002967:TDE1741|3end_penicillin-binding_protein_1795412..1795562_POSITIVE 193 77 35 85 43 NC_002967:TDE1383|3end_hypothetical_protein_1422851..1423001_POSITIVE 193 80 34 116 66 NC_002967:TDE1230|3end_hypothetical_protein_1263505..1263655_POSITIVE 191 50 5 132 92 NC_002967:TDE2521|3end_hypothetical_protein_2547955..2548105_NEGATIVE 190 100 71 29 2 NC_002967:TDE1329|3end_ATPase,_AAA_family_1365346..1365496_POSITIVE