Origin IGS: gctttaatcttaatatttcaaaacttccgttccatttaaagggcggaagtttttttatgtctttataactttccctgcattttttcttgactgttgaccatttttagaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttctaaaaatggtcaacagtcaagaaaaaatgcagggaaagttataaagacataaaaaaacttccgccctttaaatggaacggaagttttgaaatattaagattaaagc Mask Tandem Repeat Region ================================================ gctttaatcttaatatttcaaaacttccgttccatttaaagggcggaagtttttttatgtctttataactttccctgcattttttcttgactgttgaccatttttagaaa Find is-nt database================================================ Query_seq: TDE1340:TDE1341|TDE1340:TDE1341:ribosomal 5S rRNA E-loop binding protein Ctc/L25/TL5:hypothetical protein:->->:1377093..1377202 110 gctttaatcttaatatttcaaaacttccgttccatttaaagggcggaagtttttttatgtctttataactttccctgcattttttcttgactgttgaccatttttagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1340:TDE1341|TDE1340:TDE1341:ribosomal 5S rRNA E-loop binding protein Ctc/L25/TL5:hypothetical protein:->->:1377093..1377202 110 gctttaatcttaatatttcaaaacttccgttccatttaaagggcggaagtttttttatgtctttataactttccctgcattttttcttgactgttgaccatttttagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1340:TDE1341|TDE1340:TDE1341:ribosomal 5S rRNA E-loop binding protein Ctc/L25/TL5:hypothetical protein:->->:1377093..1377202 110 gctttaatcttaatatttcaaaacttccgttccatttaaagggcggaagtttttttatgtctttataactttccctgcattttttcttgactgttgaccatttttagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gctttaatcttaatatttcaaaacttccgttccatttaaagggcggaagtttttttatgtctttataactttccctgcattttttcttgactgttgaccatttttagaaa Predict ORF larger than 30AA ================================================ gctttaatcttaatatttcaaaacttccgttccatttaaagggcggaagtttttttatgtctttataactttccctgcattttttcttgactgttgaccatttttagaaa 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================================================ gctttaatcttaatatttcaaaacttccgttccatttaaagggcggaagtttttttatgtctttataactttccctgcattttttcttgactgttgaccatttttagaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1340:TDE1341|TDE1340:TDE1341:ribosomal 5S rRNA E-loop binding protein Ctc/L25/TL5:hypothetical protein:->->:1377093..1377202 110 gctttaatcttaatatttcaaaacttccgttccatttaaagggcggaagtttttttatgtctttataactttccctgcattttttcttgactgttgaccatttttagaaa Intra-Species Hit: Count: 1 Min: 1 Max: 110 Len: 110 Subject: NC_002967_TDE1340_TDE1341|ribosomal 5S rRNA E-loop binding protein Ctc/L25/TL5:hypothetical protein|POSITIVE:POSITIVE|[1377093,1377202]|110 HSP 1 e-value: 9.0E-44 bit: 176.0 Len: 110 Query Start:1 Query End:110 Subject Strand: POSITIVE Subject Start: 1 Subject End: 110 gctttaatcttaatatttcaaaacttccgttccatttaaagggcggaagnnnnnnnatgtctttataactttccctgcattttttcttgactgttgaccatttttagaaa gctttaatcttaatatttcaaaacttccgttccatttaaagggcggaagtttttttatgtctttataactttccctgcattttttcttgactgttgaccatttttagaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUUUAAUCUUAAUAUUUCAAAACUUCCGUUCCAUUUAAAGGGCGGAAGUUUUUUUAUGUCUUUAUAACUUUCCCUGCAUUUUUUCUUGACUGUUGACCAUUUUUAGAAA ((.................(((((((((((((........))))))))))))).(((((....)))))........))....(((((.((.((.....)).))..))))) (-17.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUAAAAAUGGUCAACAGUCAAGAAAAAAUGCAGGGAAAGUUAUAAAGACAUAAAAAAACUUCCGCCCUUUAAAUGGAACGGAAGUUUUGAAAUAUUAAGAUUAAAGC ..........(((((....(((...........................))).....((((((((((.((.......))..))))))))))..........))))).... (-17.23) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 90 41 71 15 NC_002967:TDE1971|5end_DNA_polymerase_III_domain_protein_1987030..1987260_NEGATIVE 291 90 41 65 1 NC_002967:TDE1916|5end_glycerol_kinase_1934767..1934997_NEGATIVE 278 105 67 68 26 NC_002967:TDE2207|5end_hypothetical_protein_2246634..2246864_NEGATIVE 277 90 42 198 140 NC_002967:TDE0410|5end_peptidase,_M48_family_462053..462283_POSITIVE 265 73 39 40 2 NC_002967:TDE2387|5end_4-alpha-glucanotransferase_2416040..2416270_POSITIVE 262 63 25 164 115 NC_002967:TDE1638|5end_dephospho-CoA_kinase,_putative_1688882..1689112_POSITIVE 253 82 41 185 145 NC_002967:TDE0481|5end_hypothetical_protein_538538..538768_NEGATIVE 252 56 16 207 164 NC_002967:TDE0125|5end_GGDEF_domain_protein_144010..144240_NEGATIVE 248 86 42 224 188 NC_002967:TDE1136|5end_M23/M37_peptidase_domain_protein_1166049..1166279_NEGATIVE 245 63 24 193 158 NC_002967:TDE0679|5end_aminotransferase,_class_V_716345..716575_POSITIVE 240 92 51 184 138 NC_002967:TDE1304|5end_hypothetical_protein_1339716..1339946_POSITIVE 240 63 23 45 9 NC_002967:TDE0588|5end_histidine_ammonia-lyase_626450..626680_POSITIVE 237 77 31 206 148 NC_002967:TDE2256|5end_hypothetical_protein_2293387..2293617_NEGATIVE 237 79 43 168 131 NC_002967:TDE1310|5end_modulator_of_DNA_gyrase_family_protein_1345962..1346192_POSITIVE 237 79 37 196 156 NC_002967:TDE1041|5end_polyribonucleotide_nucleotidyltransferase_1068324..1068554_POSITIVE 236 64 24 213 174 NC_002967:TDE1278|5end_conserved_hypothetical_protein_TIGR01440_1312788..1313018_NEGATIVE 235 64 25 187 147 NC_002967:TDE2355|5end_carbon_storage_regulator_2390838..2391068_POSITIVE 235 63 24 227 191 NC_002967:TDE0644|5end_ABC_transporter,_ATP-binding_protein_680576..680806_NEGATIVE 234 52 16 64 20 NC_002967:TDE1662|5end_replicative_DNA_helicase_1715898..1716128_POSITIVE 233 35 1 91 50 NC_002967:TDE2742|5end_site-specific_recombinase,_phage_integrase_family_2797659..2797889_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 321 53 20 71 38 NC_002967:TDE1340|3end_ribosomal_5S_rRNA_E-loop_binding_protein_Ctc/L25/TL5_1377032..1377182_POSITIVE 291 90 41 68 4 NC_002967:TDE1917|3end_cytidylyltransferase_domain_protein_1934764..1934914_NEGATIVE 281 63 21 92 47 NC_002967:TDE2706|3end_hypothetical_protein_2751916..2752066_NEGATIVE 265 73 39 43 5 NC_002967:TDE2386|3end_hypothetical_protein_2416123..2416273_POSITIVE 237 77 31 90 32 NC_002967:TDE2257|3end_5'-nucleotidase_family_protein_2293503..2293653_NEGATIVE 237 79 37 80 40 NC_002967:TDE1040|3end_ribosomal_protein_S15_1068288..1068438_POSITIVE 236 88 41 146 101 NC_002967:TDE2460|3end_aminotransferase,_class_V_2487229..2487379_POSITIVE 232 67 23 80 45 NC_002967:TDE2205|3end_enoate_reductase,_putative_2242575..2242725_NEGATIVE 231 65 21 87 52 NC_002967:TDE0449|3end_ferritin,_putative_506549..506699_NEGATIVE 227 67 22 103 64 NC_002967:TDE0794|3end_hypothetical_protein_819224..819374_NEGATIVE 226 68 24 73 32 NC_002967:TDE2574|3end_conserved_hypothetical_protein_TIGR00650_2601094..2601244_POSITIVE 225 47 20 139 110 NC_002967:TDE0401|3end_adenylate/guanylate_cyclase_catalytic_domain_protein_451837..451987_NEGATIVE 224 97 56 94 55 NC_002967:TDE2421|3end_DNA-directed_RNA_polymerase_beta_subunit_2449259..2449409_NEGATIVE 224 47 1 116 78 NC_002967:TDE1564|3end_hypothetical_protein_1616704..1616854_POSITIVE 223 45 1 119 84 NC_002967:TDE0953|3end_branched-chain_amino_acid_ABC_transporter,_permease_protein_978007..978157_POSITIVE 222 83 43 46 6 NC_002967:TDE2718|3end_magnesium_transporter_2774552..2774702_NEGATIVE 222 89 41 139 87 NC_002967:TDE0865|3end_hypothetical_protein_887599..887749_POSITIVE 221 107 61 149 111 NC_002967:TDE1642|3end_hypothetical_protein_1692771..1692921_NEGATIVE 221 54 14 146 112 NC_002967:TDE1392|3end_hypothetical_protein_1432573..1432723_POSITIVE 219 56 23 128 96 NC_002967:TDE2751|3end_hypothetical_protein_2809194..2809344_POSITIVE