Origin IGS: atttcatattatacactatttcctttgacaaaacaagaacttttttgtatcatatcaaaagaatatttgttctaactttatgttccggcggcaagatagaaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atttctatcttgccgccggaacataaagttagaacaaatattcttttgatatgatacaaaaaagttcttgttttgtcaaaggaaatagtgtataatatgaaat Mask Tandem Repeat Region ================================================ atttcatattatacactatttcctttgacaaaacaagaacttttttgtatcatatcaaaagaatatttgttctaactttatgttccggcggcaagatagaaat Find is-nt database================================================ Query_seq: TDE0114:TDE0115|TDE0114:TDE0115:iron-dependent transcriptional regulator:hypothetical protein:<-->:134091..134193 103 atttcatattatacactatttcctttgacaaaacaagaacttttttgtatcatatcaaaagaatatttgttctaactttatgttccggcggcaagatagaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0114:TDE0115|TDE0114:TDE0115:iron-dependent transcriptional regulator:hypothetical protein:<-->:134091..134193 103 atttcatattatacactatttcctttgacaaaacaagaacttttttgtatcatatcaaaagaatatttgttctaactttatgttccggcggcaagatagaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0114:TDE0115|TDE0114:TDE0115:iron-dependent transcriptional regulator:hypothetical protein:<-->:134091..134193 103 atttcatattatacactatttcctttgacaaaacaagaacttttttgtatcatatcaaaagaatatttgttctaactttatgttccggcggcaagatagaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttcatattatacactatttcctttgacaaaacaagaacttttttgtatcatatcaaaagaatatttgttctaactttatgttccggcggcaagatagaaat Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 6 End: 101 ..... M L Y T I S F D K T R T F L Y H I K R I F V L T L C S G G K I E .. atttcatattatacactatttcctttgacaaaacaagaacttttttgtatcatatcaaaagaatatttgttctaactttatgttccggcggcaagatagaaat 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: 92 Start: 24 End: 53 .......................TTTGACAAAACAAGAACTTTTTTGTATCAT.................................................. PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 8 End: 37 .......CTTGTTTTGTCAAAGGAAATAGTGTATAAT.................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atttcatattatacactatttcctttgacaaaacaagaacttttttgtatcatatcaaaagaatatttgttctaactttatgttccggcggcaagatagaaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0114:TDE0115|TDE0114:TDE0115:iron-dependent transcriptional regulator:hypothetical protein:<-->:134091..134193 103 atttcatattatacactatttcctttgacaaaacaagaacttttttgtatcatatcaaaagaatatttgttctaactttatgttccggcggcaagatagaaat Intra-Species Hit: Count: 1 Min: 1 Max: 103 Len: 103 Subject: NC_002967_TDE0114_TDE0115|iron-dependent transcriptional regulator:hypothetical protein|NEGATIVE:POSITIVE|[134091,134193]|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 atttcatattatacactatttcctttgacaaaacaagaacttttttgtatcatatcaaaagaatatttgttctaactttatgttccggcggcaagatagaaat atttcatattatacactatttcctttgacaaaacaagaacttttttgtatcatatcaaaagaatatttgttctaactttatgttccggcggcaagatagaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUCAUAUUAUACACUAUUUCCUUUGACAAAACAAGAACUUUUUUGUAUCAUAUCAAAAGAAUAUUUGUUCUAACUUUAUGUUCCGGCGGCAAGAUAGAAAU ...............((((((((.(((.....((((((....))))))..((((.....(((((....))))).....))))...))).))..)))))).... (-11.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUCUAUCUUGCCGCCGGAACAUAAAGUUAGAACAAAUAUUCUUUUGAUAUGAUACAAAAAAGUUCUUGUUUUGUCAAAGGAAAUAGUGUAUAAUAUGAAAU ((((((((..((((.....(((.....)))..........(((((((((((....((((........))))..)))))))))))...).)))..))).))))) (-16.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 808 100 51 191 142 NC_002967:TDE0114|5end_iron-dependent_transcriptional_regulator_134000..134230_NEGATIVE 253 92 52 169 119 NC_002967:TDE1544|5end_mannosyltransferase,_putative_1587154..1587384_POSITIVE 251 93 80 129 116 NC_002967:TDE0546|5end_hypothetical_protein_584909..585139_POSITIVE 244 99 71 173 142 NC_002967:TDE2399|5end_ribonuclease_P_protein_component_2426160..2426390_NEGATIVE 238 92 68 120 91 NC_002967:TDE0833|5end_lipoprotein,_putative_852992..853222_POSITIVE 231 94 66 170 141 NC_002967:TDE1579|5end_fibronectin/fibrinogen-binding_protein,_internal_deletion_1627489..1627719_NEGATIVE 229 92 53 165 120 NC_002967:TDE2086|5end_DnaJ_domain_protein_2114877..2115107_POSITIVE 226 98 75 98 68 NC_002967:TDE2637|5end_hypothetical_protein_2677316..2677546_NEGATIVE 226 100 84 22 6 NC_002967:TDE0537|5end_hypothetical_protein_579024..579254_POSITIVE 226 89 41 184 134 NC_002967:TDE0510|5end_hypothetical_protein_561081..561311_NEGATIVE 221 99 61 64 8 NC_002967:TDE0570|5end_hypothetical_protein_600169..600399_POSITIVE 220 100 64 81 40 NC_002967:TDE1383|5end_hypothetical_protein_1422301..1422531_POSITIVE 208 100 54 174 128 NC_002967:TDE0173|5end_FtsK/SpoIIIE_family_protein_203970..204200_POSITIVE 207 93 54 148 101 NC_002967:TDE1024|5end_conserved_hypothetical_protein_TIGR01319_1055575..1055805_POSITIVE 204 97 71 157 128 NC_002967:TDE2066|5end_exodeoxyribonuclease_VII,_small_subunit_2091906..2092136_POSITIVE 199 100 74 45 14 NC_002967:TDE0899|5end_ABC_transporter,_permease_protein,_putative_916481..916711_POSITIVE 198 97 59 179 132 NC_002967:TDE0614|5end_precorrin-4_C11-methyltransferase_647987..648217_POSITIVE 195 58 16 113 67 NC_002967:TDE1417|5end_ABC_transporter,_ATP-binding_protein_1460656..1460886_POSITIVE 195 85 48 225 185 NC_002967:TDE0789|5end_30S_ribosomal_protein_S13_816562..816792_POSITIVE 195 85 48 95 55 NC_002967:TDE0788|5end_ribosomal_protein_L36_816432..816662_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 92 52 105 55 NC_002967:TDE1543|3end_conserved_hypothetical_protein_TIGR00247_1587170..1587320_POSITIVE 251 93 80 110 97 NC_002967:TDE0545|3end_hypothetical_protein_584970..585120_POSITIVE 238 92 68 123 94 NC_002967:TDE0832|3end_hypothetical_protein_853075..853225_POSITIVE 227 61 30 63 30 NC_002967:TDE2253|3end_hypothetical_protein_2291499..2291649_POSITIVE 220 100 64 133 92 NC_002967:TDE1382|3end_transcriptional_regulator,_ArsR_family_1422433..1422583_POSITIVE 217 95 66 120 95 NC_002967:TDE0610|3end_3-hydroxyacyl-CoA_dehydrogenase,_putative_646357..646507_NEGATIVE 210 87 41 151 105 NC_002967:TDE0511|3end_hypothetical_protein_561110..561260_NEGATIVE 208 100 54 149 103 NC_002967:TDE0172|3end_undecaprenyl_pyrophosphate_phosphatase_204025..204175_POSITIVE 207 93 54 115 68 NC_002967:TDE1023|3end_methylaspartate_mutase_subunit_S_1055622..1055772_POSITIVE 206 99 70 128 100 NC_002967:TDE2422|3end_ribosomal_protein_L7/L12_2452911..2453061_NEGATIVE 204 100 55 146 105 NC_002967:TDE1084|3end_folylpolyglutamate_synthetase,_putative_1114934..1115084_NEGATIVE 201 92 64 138 106 NC_002967:TDE0820|3end_transcriptional_regulator,_TetR_family_843714..843864_NEGATIVE 199 100 74 41 10 NC_002967:TDE0898|3end_hypothetical_protein_916557..916707_POSITIVE 195 58 16 104 58 NC_002967:TDE1416|3end_ABC_transporter,_permease_protein_1460727..1460877_POSITIVE 195 85 48 47 7 NC_002967:TDE0787|3end_preprotein_translocase_SecY_816464..816614_POSITIVE 192 100 52 49 1 NC_002967:TDE1290|3end_hypothetical_protein_1328648..1328798_POSITIVE 191 89 41 78 31 NC_002967:TDE1815|3end_hypothetical_protein_1849458..1849608_NEGATIVE 190 79 33 129 81 NC_002967:TDE1951|3end_ribonuclease_Z_1967403..1967553_NEGATIVE 190 92 55 129 81 NC_002967:TDE1160|3end_hypothetical_protein_1194417..1194567_NEGATIVE 190 100 66 137 104 NC_002967:TDE0211|3end_ABC_transporter,_permease_protein,_cysTW_family_246555..246705_NEGATIVE