Origin IGS: agcgttttgataacgagttttactatctctcgacagtcgaaagaatagacatgttaggaaaccggcatactgaaactatacgatgccgacaggacattttactttgtatttgcttcctatacaaattagggaaagaagattaaaggtcgtgatagaggaaaaaaagaagaaaaatattctgatattccgtgaggtgtca .........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 tgacacctcacggaatatcagaatatttttcttctttttttcctctatcacgacctttaatcttctttccctaatttgtataggaagcaaatacaaagtaaaatgtcctgtcggcatcgtatagtttcagtatgccggtttcctaacatgtctattctttcgactgtcgagagatagtaaaactcgttatcaaaacgct Mask Tandem Repeat Region ================================================ agcgttttgataacgagttttactatctctcgacagtcgaaagaatagacatgttaggaaaccggcatactgaaactatacgatgccgacaggacattttactttgtatttgcttcctatacaaattagggaaagaagattaaaggtcgtgatagaggaaaaaaagaagaaaaatattctgatattccgtgaggtgtca Find is-nt database================================================ Query_seq: TF0572:TF0573|TF0572:TF0573:hypothetical protein:DNA polymerase III, delta subunit:->->:603691..603889 199 agcgttttgataacgagttttactatctctcgacagtcgaaagaatagacatgttaggaaaccggcatactgaaactatacgatgccgacaggacattttactttgtatttgcttcctatacaaattagggaaagaagattaaaggtcgtgatagaggaaaaaaagaagaaaaatattctgatattccgtgaggtgtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0572:TF0573|TF0572:TF0573:hypothetical protein:DNA polymerase III, delta subunit:->->:603691..603889 199 agcgttttgataacgagttttactatctctcgacagtcgaaagaatagacatgttaggaaaccggcatactgaaactatacgatgccgacaggacattttactttgtatttgcttcctatacaaattagggaaagaagattaaaggtcgtgatagaggaaaaaaagaagaaaaatattctgatattccgtgaggtgtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0572:TF0573|TF0572:TF0573:hypothetical protein:DNA polymerase III, delta subunit:->->:603691..603889 199 agcgttttgataacgagttttactatctctcgacagtcgaaagaatagacatgttaggaaaccggcatactgaaactatacgatgccgacaggacattttactttgtatttgcttcctatacaaattagggaaagaagattaaaggtcgtgatagaggaaaaaaagaagaaaaatattctgatattccgtgaggtgtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcgttttgataacgagttttactatctctcgacagtcgaaagaatagacatgttaggaaaccggcatactgaaactatacgatgccgacaggacattttactttgtatttgcttcctatacaaattagggaaagaagattaaaggtcgtgatagaggaaaaaaagaagaaaaatattctgatattccgtgaggtgtca Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 45 End: 140 ............................................ M D M L G N R H T E T I R C R Q D I L L C I C F L Y K L G K E D ........................................................... Protein_Len: 39 Strand: + Start: 83 End: 199 .................................................................................. M P T G H F T L Y L L P I Q I R E R R L K V V I E E K K K K N I L I F R E V S Protein_Len: 35 Strand: - Start: 79 End: 183 .............................................................................. V I G V P C K V K Y K S G I C I L S L L N F T T I S S F F F F F I R M ................ Protein_Len: 33 Strand: - Start: 26 End: 124 ......................... R E V T S L I S M N P F R C V S V I R H R C S M K S Q I Q K R Y M ........................................................................... agcgttttgataacgagttttactatctctcgacagtcgaaagaatagacatgttaggaaaccggcatactgaaactatacgatgccgacaggacattttactttgtatttgcttcctatacaaattagggaaagaagattaaaggtcgtgatagaggaaaaaaagaagaaaaatattctgatattccgtgaggtgtca 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================================================ agcgttttgataacgagttttactatctctcgacagtcgaaagaatagacatgttaggaaaccggcatactgaaactatacgatgccgacaggacattttactttgtatttgcttcctatacaaattagggaaagaagattaaaggtcgtgatagaggaaaaaaagaagaaaaatattctgatattccgtgaggtgtca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0572:TF0573|TF0572:TF0573:hypothetical protein:DNA polymerase III, delta subunit:->->:603691..603889 199 agcgttttgataacgagttttactatctctcgacagtcgaaagaatagacatgttaggaaaccggcatactgaaactatacgatgccgacaggacattttactttgtatttgcttcctatacaaattagggaaagaagattaaaggtcgtgatagaggaaaaaaagaagaaaaatattctgatattccgtgaggtgtca Intra-Species Hit: Count: 1 Min: 1 Max: 199 Len: 199 Subject: tfor_TF0572_TF0573|hypothetical protein:DNA polymerase III, delta subunit|POSITIVE:POSITIVE|[603691,603889]|199 HSP 1 e-value: 1.0E-96 bit: 353.0 Len: 199 Query Start:1 Query End:199 Subject Strand: POSITIVE Subject Start: 1 Subject End: 199 agcgttttgataacgagttttactatctctcgacagtcgaaagaatagacatgttaggaaaccggcatactgaaactatacgatgccgacaggacattttactttgtatttgcttcctatacaaattagggaaagaagattaaaggtcgtgatagaggnnnnnnngaagaaaaatattctgatattccgtgaggtgtca agcgttttgataacgagttttactatctctcgacagtcgaaagaatagacatgttaggaaaccggcatactgaaactatacgatgccgacaggacattttactttgtatttgcttcctatacaaattagggaaagaagattaaaggtcgtgatagaggaaaaaaagaagaaaaatattctgatattccgtgaggtgtca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCGUUUUGAUAACGAGUUUUACUAUCUCUCGACAGUCGAAAGAAUAGACAUGUUAGGAAACCGGCAUACUGAAACUAUACGAUGCCGACAGGACAUUUUACUUUGUAUUUGCUUCCUAUACAAAUUAGGGAAAGAAGAUUAAAGGUCGUGAUAGAGGAAAAAAAGAAGAAAAAUAUUCUGAUAUUCCGUGAGGUGUCA ..((((.....)))).((((((((((((.(((.....))).)).))))..((((..(....)..))))..)))))).....((((((..((.(((......(((((..(((..((((((.......))))))..)))...)))))))).)).....((((....((((........))))....))))....)))))). (-45.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGACACCUCACGGAAUAUCAGAAUAUUUUUCUUCUUUUUUUCCUCUAUCACGACCUUUAAUCUUCUUUCCCUAAUUUGUAUAGGAAGCAAAUACAAAGUAAAAUGUCCUGUCGGCAUCGUAUAGUUUCAGUAUGCCGGUUUCCUAACAUGUCUAUUCUUUCGACUGUCGAGAGAUAGUAAAACUCGUUAUCAAAACGCU (((........((((....((((........))))....))))......((((..((((.................(((.((((((((....(((........))).....(((((((...........).)))))))))))))))))...((((.((((((.....))))))))))))))..))))..)))....... (-34.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 317 89 49 229 191 tfor:TF2760|5end_MarR__family_transcriptional_regulator_2945019..2945249_POSITIVE 312 99 54 72 24 tfor:TF2399|5end_precorrin-2_methyltransferase_2571250..2571480_POSITIVE 307 98 56 121 69 tfor:TF2466|5end_pyruvate_kinase_2644385..2644615_POSITIVE 289 99 56 92 45 tfor:TF1735|5end_dehydrogenase,_possible_NADH-dependent_dehydrogenase_1860127..1860357_POSITIVE 287 66 23 87 40 tfor:TF2345|5end_dGTP_triphosphohydrolase_2508372..2508602_POSITIVE 287 90 51 128 91 tfor:TF1462|5end_erythronate-4-phosphate_dehydrogenase_1552184..1552414_POSITIVE 286 95 57 65 21 tfor:TF3028|5end_1-deoxy-d-xylulose-5-phosphate_reductoisomerase_3251642..3251872_POSITIVE 285 95 51 66 27 tfor:TF2719|5end_hypothetical_protein_2892701..2892931_POSITIVE 282 94 53 219 171 tfor:TF2707|5end_glutamine_amidotransferase_2878305..2878535_POSITIVE 281 93 51 62 11 tfor:TF2454|5end_D-alanyl-D-alanine_dipeptidase_2631259..2631489_POSITIVE 279 44 2 69 23 tfor:TF0973|5end_conserved_hypothetical_protein_1023263..1023493_POSITIVE 274 66 21 74 29 tfor:TF1164|5end_two-component_system_sensor_histidine_kinase_1243682..1243912_POSITIVE 274 168 121 161 116 tfor:TF0092|5end_outer_membrane_protein_98889..99119_POSITIVE 273 93 58 61 28 tfor:TF2850|5end_endoribonuclease_L-PSP_3038417..3038647_POSITIVE 273 108 63 47 3 tfor:TF1508|5end_anti-sigma_factor_1616345..1616575_POSITIVE 271 96 65 138 98 tfor:TF0864|5end_O-succinylbenzoate--CoA_ligase_914570..914800_POSITIVE 269 98 56 53 3 tfor:TF2302|5end_conserved_hypothetical_protein;_possible_outer_membrane_protein_2456628..2456858_POSITIVE 267 97 63 212 176 tfor:TF2020|5end_muconate_cycloisomerase_2176321..2176551_POSITIVE 264 95 58 53 14 tfor:TF2074|5end_pyridoxal-phosphate-dependent_aminotransferase_2239719..2239949_POSITIVE 263 78 32 163 117 tfor:TF1919|5end_hypothetical_protein_2070037..2070267_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 98 56 99 47 tfor:TF2465|3end_O-methyltransferase_2644443..2644593_POSITIVE 289 116 81 78 48 tfor:TF1815|3end_conserved_hypothetical_protein_1957442..1957592_POSITIVE 287 66 23 69 22 tfor:TF2344|3end_ATP/GTP_binding_protein_2508434..2508584_POSITIVE 287 90 51 117 80 tfor:TF1461|3end_DNA-damage-inducible_protein_F_1552253..1552403_POSITIVE 285 95 51 96 57 tfor:TF2718|3end_hypothetical_protein_2892811..2892961_POSITIVE 274 66 21 83 38 tfor:TF1163|3end_two-component_system_response_regulator_1243771..1243921_POSITIVE 274 168 121 109 64 tfor:TF0091|3end_outer_membrane_protein_98917..99067_POSITIVE 266 89 43 101 35 tfor:TF2850|3end_endoribonuclease_L-PSP_3038871..3039021_POSITIVE 266 41 6 149 108 tfor:TF0629|3end_hypothetical_protein_666710..666860_POSITIVE 264 93 56 49 13 tfor:TF2453|3end_glutamate_racemase_2631326..2631476_POSITIVE 264 95 58 46 7 tfor:TF2073|3end_conserved_hypothetical_protein_2239792..2239942_POSITIVE 263 78 32 151 105 tfor:TF1918|3end_hypothetical_protein_2070105..2070255_POSITIVE 259 170 122 110 65 tfor:TF2923|3end_hypothetical_protein_3122403..3122553_POSITIVE 257 107 63 149 109 tfor:TF2335|3end_conserved_hypothetical_protein_2496177..2496327_POSITIVE 257 74 34 86 40 tfor:TF0784|3end_possible_biopolymer_transport_protein_837881..838031_POSITIVE 254 97 52 66 21 tfor:TF2444|3end_regulatory_protein_RecX_2621549..2621699_POSITIVE 254 74 32 128 94 tfor:TF0218|3end_translation_initiation_factor_3_(IF-3)_243891..244041_POSITIVE 253 88 41 135 98 tfor:TF1401|3end_Holliday_junction_DNA_helicase_1477610..1477760_POSITIVE 253 41 1 143 100 tfor:TF0012|3end_conserved_hypothetical_protein_6641..6791_POSITIVE 251 69 27 126 86 tfor:TF2593|3end_amino_acid_transport_protein_2764242..2764392_POSITIVE