Origin IGS: ttcgccgttcaggtctaattctttgacttcttgttctgacatttttgtttacctttcatttttaactttaaaaaacgttcttaaaaacgaccgcactttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaagtgcggtcgtttttaagaacgttttttaaagttaaaaatgaaaggtaaacaaaaatgtcagaacaagaagtcaaagaattagacctgaacggcgaa Mask Tandem Repeat Region ================================================ ttcgccgttcaggtctaattctttgacttcttgttctgacatttttgtttacctttcatttttaactttaaaaaacgttcttaaaaacgaccgcactttta Find is-nt database================================================ Query_seq: AA01743:AA01744|AA01743:AA01744:lysyl-tRNA synthetase:peptide chain release factor RF-2:->->:1179412..1179512 101 ttcgccgttcaggtctaattctttgacttcttgttctgacatttttgtttacctttcatttttaactttaaaaaacgttcttaaaaacgaccgcactttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01743:AA01744|AA01743:AA01744:lysyl-tRNA synthetase:peptide chain release factor RF-2:->->:1179412..1179512 101 ttcgccgttcaggtctaattctttgacttcttgttctgacatttttgtttacctttcatttttaactttaaaaaacgttcttaaaaacgaccgcactttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01743:AA01744|AA01743:AA01744:lysyl-tRNA synthetase:peptide chain release factor RF-2:->->:1179412..1179512 101 ttcgccgttcaggtctaattctttgacttcttgttctgacatttttgtttacctttcatttttaactttaaaaaacgttcttaaaaacgaccgcactttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcgccgttcaggtctaattctttgacttcttgttctgacatttttgtttacctttcatttttaactttaaaaaacgttcttaaaaacgaccgcactttta Predict ORF larger than 30AA ================================================ ttcgccgttcaggtctaattctttgacttcttgttctgacatttttgtttacctttcatttttaactttaaaaaacgttcttaaaaacgaccgcactttta 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================================================ ttcgccgttcaggtctaattctttgacttcttgttctgacatttttgtttacctttcatttttaactttaaaaaacgttcttaaaaacgaccgcactttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA01743:AA01744|AA01743:AA01744:lysyl-tRNA synthetase:peptide chain release factor RF-2:->->:1179412..1179512 101 ttcgccgttcaggtctaattctttgacttcttgttctgacatttttgtttacctttcatttttaactttaaaaaacgttcttaaaaacgaccgcactttta Intra-Species Hit: Count: 1 Min: 1 Max: 101 Len: 101 Subject: aact_AA01743_AA01744|lysyl-tRNA synthetase:peptide chain release factor RF-2|POSITIVE:POSITIVE|[1179412,1179512]|101 HSP 1 e-value: 6.0E-51 bit: 200.0 Len: 101 Query Start:1 Query End:101 Subject Strand: POSITIVE Subject Start: 1 Subject End: 101 ttcgccgttcaggtctaattctttgacttcttgttctgacatttttgtttacctttcatttttaactttaaaaaacgttcttaaaaacgaccgcactttta ttcgccgttcaggtctaattctttgacttcttgttctgacatttttgtttacctttcatttttaactttaaaaaacgttcttaaaaacgaccgcactttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCGCCGUUCAGGUCUAAUUCUUUGACUUCUUGUUCUGACAUUUUUGUUUACCUUUCAUUUUUAACUUUAAAAAACGUUCUUAAAAACGACCGCACUUUUA ...........((((.................((...((((....)))).))......((((((....))))))..............))))......... ( -8.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAGUGCGGUCGUUUUUAAGAACGUUUUUUAAAGUUAAAAAUGAAAGGUAAACAAAAAUGUCAGAACAAGAAGUCAAAGAAUUAGACCUGAACGGCGAA ..........(((((((.......(((((((.......)))))))..((((.........((.(..........).)).........)))))))))))... (-12.17) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 416 99 55 143 100 aact:AA01248|5end_conserved_hypothetical_protein_(possible_phosphoesterase)_849734..849964_POSITIVE 416 99 55 73 30 aact:AA01247|5end_hypothetical_protein_849664..849894_POSITIVE 408 100 67 123 90 aact:AA00792|5end_conserved_hypothetical_protein_543142..543372_POSITIVE 377 100 68 95 63 aact:AA00733|5end_hypothetical_protein_502335..502565_POSITIVE 361 100 54 124 77 aact:AA01994|5end_chorismate_mutase;_prephenate_dehydrogenase_1354959..1355189_POSITIVE 354 100 66 177 144 aact:AA00212|5end_ribokinase_146056..146286_POSITIVE 354 100 66 76 43 aact:AA00211|5end_hypothetical_protein_145955..146185_POSITIVE 339 100 72 138 110 aact:AA02410|5end_cell_division_protein_1655429..1655659_POSITIVE 336 100 51 123 64 aact:AA02937|5end_conserved_hypothetical_protein_2056379..2056609_POSITIVE 328 100 64 123 87 aact:AA00404|5end_conserved_hypothetical_protein_269822..270052_POSITIVE 327 100 66 155 120 aact:AA02409|5end_DNA_ligase_1653315..1653545_POSITIVE 325 100 52 79 31 aact:AA01986|5end_pyruvate_dehydrogenase_complex_E2_1348753..1348983_POSITIVE 322 99 71 124 96 aact:AA02716|5end_peptidase_T_1899789..1900019_POSITIVE 322 100 52 222 171 aact:AA01424|5end_threonine_deaminase_(dehydratase)_957740..957970_POSITIVE 319 100 66 224 188 aact:AA00579|5end_probable_DNA_recombination_protein_395265..395495_POSITIVE 317 100 54 178 135 aact:AA02030|5end_threonyl-tRNA_synthetase_1382171..1382401_POSITIVE 306 100 67 152 119 aact:AA01648|5end_alpha-amylase_protein;_1,4-alpha-D-glucan_glucanohydrolase_1115170..1115400_POSITIVE 306 100 67 51 18 aact:AA01646|5end_hypothetical_protein_1115069..1115299_POSITIVE 305 99 71 162 134 aact:AA00130|5end_mercuric_transport_protein_(periplasmic_mercury_ion_binding_protein)_(mercury_scavenger_protein)_94217..94447_POSITIVE 305 99 71 67 39 aact:AA00129|5end_hypothetical_protein_94122..94352_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 408 100 67 35 2 aact:AA00790|3end_recombination_DNA_repair_protein_543134..543284_POSITIVE 398 100 51 145 94 aact:AA02169|3end_hypothetical_protein_1484664..1484814_POSITIVE 377 100 68 107 75 aact:AA00732|3end_citrate_lyase_ligase_502427..502577_POSITIVE 361 100 54 89 42 aact:AA01992|3end_protease_IV;_signal_peptide_peptidase;_Endopeptidase_IV_1355004..1355154_POSITIVE 360 100 60 130 91 aact:AA01259|3end_protoporphyrinogen_oxidase_854943..855093_POSITIVE 356 100 51 84 37 aact:AA02443|3end_cytochrome_C_related_protein_1686590..1686740_POSITIVE 356 100 51 129 82 aact:AA02444|3end_hypothetical_protein_1686635..1686785_POSITIVE 354 100 66 73 40 aact:AA00209|3end_D-ribose_ABC_transporter,_periplasmic-binding_protein_146032..146182_POSITIVE 339 100 72 33 5 aact:AA02409|3end_DNA_ligase_1655404..1655554_POSITIVE 328 100 64 69 33 aact:AA00402|3end_conserved_hypothetical_protein_(possible_periplasmic_protein)_269848..269998_POSITIVE 322 99 71 42 14 aact:AA02715|3end_paraquat-inducible_protein_pqiB_homolog_1899787..1899937_POSITIVE 322 100 52 82 31 aact:AA01423|3end_cell_division_protein_X,_ABC_system_permease_957680..957830_POSITIVE 319 100 66 80 44 aact:AA00578|3end_DNA_topoisomerase_395201..395351_POSITIVE 317 100 54 142 99 aact:AA02029|3end_hypothetical_protein_1382215..1382365_POSITIVE 316 100 60 137 97 aact:AA00528|3end_conserved_hypothetical_protein_361703..361853_POSITIVE 315 100 68 37 5 aact:AA02936|3end_lipoprotein_E_precursor;_outer_membrane_protein_P4_precursor;_acid_phosphatase_2056373..2056523_POSITIVE 308 100 54 47 2 aact:AA01985|3end_pyruvate_dehydrogenase,_E1_component_1348801..1348951_POSITIVE 306 100 67 86 53 aact:AA01645|3end_ferric_transport_ABC-related_ATP-binding_protein_1115184..1115334_POSITIVE 305 99 71 72 44 aact:AA00128|3end_cation-transporting_ATPase_(probable_potassium/copper_transporter)_94207..94357_POSITIVE 296 99 68 144 113 aact:AA00507|3end_hypothetical_protein_353201..353351_POSITIVE