Origin IGS: tatagcaaggcttggcgaatcgcagaaacgttctcaaaaacattctgaaaaccgaccgcactttttgccgaatgttgcggataaaaaaagcagagatcgctctctgctttttgaaaaacgtataaaatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taattttatacgtttttcaaaaagcagagagcgatctctgctttttttatccgcaacattcggcaaaaagtgcggtcggttttcagaatgtttttgagaacgtttctgcgattcgccaagccttgctata Mask Tandem Repeat Region ================================================ tatagcaaggcttggcgaatcgcagaaacgttctcaaaaacattctgaaaaccgaccgcactttttgccgaatgttgcggataaaaaaagcagagatcgctctctgctttttgaaaaacgtataaaatta Find is-nt database================================================ Query_seq: AA02260:AA02261|AA02260:AA02261:pseudouridylate synthase I:30S ribosomal protein S9:->->:1538023..1538152 130 tatagcaaggcttggcgaatcgcagaaacgttctcaaaaacattctgaaaaccgaccgcactttttgccgaatgttgcggataaaaaaagcagagatcgctctctgctttttgaaaaacgtataaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA02260:AA02261|AA02260:AA02261:pseudouridylate synthase I:30S ribosomal protein S9:->->:1538023..1538152 130 tatagcaaggcttggcgaatcgcagaaacgttctcaaaaacattctgaaaaccgaccgcactttttgccgaatgttgcggataaaaaaagcagagatcgctctctgctttttgaaaaacgtataaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA02260:AA02261|AA02260:AA02261:pseudouridylate synthase I:30S ribosomal protein S9:->->:1538023..1538152 130 tatagcaaggcttggcgaatcgcagaaacgttctcaaaaacattctgaaaaccgaccgcactttttgccgaatgttgcggataaaaaaagcagagatcgctctctgctttttgaaaaacgtataaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatagcaaggcttggcgaatcgcagaaacgttctcaaaaacattctgaaaaccgaccgcactttttgccgaatgttgcggataaaaaaagcagagatcgctctctgctttttgaaaaacgtataaaatta Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 12 End: 122 ........... M A N R R N V L K N I L K T D R T F C R M L R I K K A E I A L C F L K N V ........ Protein_Len: 43 Strand: + Start: 2 End: 130 . M A R L G E S Q K R S Q K H S E N R P H F L P N V A D K K S R D R S L L F E K R I K L Protein_Len: 42 Strand: - Start: 3 End: 128 .. L L A Q R I A S V N E F V N Q F G V A S K A S H Q P Y F F C L D S E A K Q F V Y L M .. Protein_Len: 32 Strand: - Start: 2 End: 97 . Y C P K A F R L F T R L F M R F V S R V K Q R I N R I F F A S M ................................. tatagcaaggcttggcgaatcgcagaaacgttctcaaaaacattctgaaaaccgaccgcactttttgccgaatgttgcggataaaaaaagcagagatcgctctctgctttttgaaaaacgtataaaatta 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================================================ tatagcaaggcttggcgaatcgcagaaacgttctcaaaaacattctgaaaaccgaccgcactttttgccgaatgttgcggataaaaaaagcagagatcgctctctgctttttgaaaaacgtataaaatta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 89 HP_score: -9.9 Tail_Score: -4.57073 Start: 90 End: 107 Full_Region: TTGCGGATAAAAAAA GCAGAGA TCGC TCTCTGC TTTTTGAAAAACGTA .........................................................................................GCAGAGATCGCTCTCTGC....................... Find igs database================================================ Query_seq: AA02260:AA02261|AA02260:AA02261:pseudouridylate synthase I:30S ribosomal protein S9:->->:1538023..1538152 130 tatagcaaggcttggcgaatcgcagaaacgttctcaaaaacattctgaaaaccgaccgcactttttgccgaatgttgcggataaaaaaagcagagatcgctctctgctttttgaaaaacgtataaaatta Intra-Species Hit: Count: 1 Min: 1 Max: 130 Len: 130 Subject: aact_AA02260_AA02261|pseudouridylate synthase I:30S ribosomal protein S9|POSITIVE:POSITIVE|[1538023,1538152]|130 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 130 Query Start:1 Query End:130 Subject Strand: POSITIVE Subject Start: 1 Subject End: 130 tatagcaaggcttggcgaatcgcagaaacgttctcaaaaacattctgaaaaccgaccgcactttttgccgaatgttgcggatnnnnnnngcagagatcgctctctgctttttgaaaaacgtataaaatta tatagcaaggcttggcgaatcgcagaaacgttctcaaaaacattctgaaaaccgaccgcactttttgccgaatgttgcggataaaaaaagcagagatcgctctctgctttttgaaaaacgtataaaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAGCAAGGCUUGGCGAAUCGCAGAAACGUUCUCAAAAACAUUCUGAAAACCGACCGCACUUUUUGCCGAAUGUUGCGGAUAAAAAAAGCAGAGAUCGCUCUCUGCUUUUUGAAAAACGUAUAAAAUUA ....((((.(.((((((((((((((((..(((......))).))))).....)))........)))))))).).))))......((((((((((((....)))))))))))).................. (-32.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUUUAUACGUUUUUCAAAAAGCAGAGAGCGAUCUCUGCUUUUUUUAUCCGCAACAUUCGGCAAAAAGUGCGGUCGGUUUUCAGAAUGUUUUUGAGAACGUUUCUGCGAUUCGCCAAGCCUUGCUAUA ..................((((((((((((....))))))))))))......((((..((.(((......(((((...(((((((((.....)))))))))....)))))....))).))..)))).... (-36.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 497 77 35 162 121 aact:AA00324|5end_tRNA_(Uracil-5-)-methyltransferase_(tRNA(M-5-U54)-methyltransferase)_220147..220377_POSITIVE 476 80 36 150 98 aact:AA01436|5end_fructose-bisphosphate_aldolase_class_II_962981..963211_POSITIVE 448 66 23 176 127 aact:AA00819|5end_D-alanyl-D-alanine_carboxypeptidase_562644..562874_POSITIVE 426 67 28 196 151 aact:AA00268|5end_acyl_carrier_protein_(ACP)_188104..188334_POSITIVE 421 67 21 179 133 aact:AA00212|5end_ribokinase_146056..146286_POSITIVE 421 67 21 78 32 aact:AA00211|5end_hypothetical_protein_145955..146185_POSITIVE 414 69 22 196 148 aact:AA01635|5end_ribonucleoside_diphosphate_reductase,_beta_chain_1104615..1104845_POSITIVE 412 69 22 172 133 aact:AA01458|5end_aminotransferase_978820..979050_POSITIVE 410 80 48 101 62 aact:AA01986|5end_pyruvate_dehydrogenase_complex_E2_1348753..1348983_POSITIVE 410 67 29 45 1 aact:AA00267|5end_hypothetical_protein_187953..188183_POSITIVE 403 70 30 161 117 aact:AA02409|5end_DNA_ligase_1653315..1653545_POSITIVE 399 69 21 231 178 aact:AA01810|5end_electron_transport_complex_protein_1219250..1219480_POSITIVE 394 69 29 163 127 aact:AA02673|5end_gluconate_utilization_operon_repressor_1858913..1859143_POSITIVE 387 70 21 205 160 aact:AA03000|5end_uracil-DNA_glycosylase_(UDG)_2095076..2095306_POSITIVE 386 69 21 82 36 aact:AA00952|5end_hemY_protein_homolog_657541..657771_POSITIVE 385 78 36 187 141 aact:AA01918|5end_anaerobic_C4-dicarboxylate_transporter_1290931..1291161_POSITIVE 373 94 51 89 43 aact:AA00365|5end_30S_ribosomal_protein_S19_245914..246144_POSITIVE 372 80 35 157 110 aact:AA00409|5end_methionyl-tRNA_formyltransferase_273611..273841_POSITIVE 370 80 36 134 95 aact:AA00401|5end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_slyD_(PPiase)_268361..268591_POSITIVE 368 80 31 162 99 aact:AA00419|5end_conserved_hypothetical_protein_(possible_phosphatidylethanolamine-binding_protein)_284337..284567_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 482 79 33 148 97 aact:AA01259|3end_protoporphyrinogen_oxidase_854943..855093_POSITIVE 476 80 36 110 58 aact:AA01434|3end_conserved_hypothetical_protein_(possible_o-antigen_ligase)_963021..963171_POSITIVE 439 70 35 151 116 aact:AA00323|3end_conserved_hypothetical_protein_(possible_SAM-dependent_methyltransferase)_220222..220372_POSITIVE 423 80 33 149 103 aact:AA00528|3end_conserved_hypothetical_protein_361703..361853_POSITIVE 421 67 21 75 29 aact:AA00209|3end_D-ribose_ABC_transporter,_periplasmic-binding_protein_146032..146182_POSITIVE 419 69 30 86 48 aact:AA02443|3end_cytochrome_C_related_protein_1686590..1686740_POSITIVE 419 69 30 131 93 aact:AA02444|3end_hypothetical_protein_1686635..1686785_POSITIVE 412 69 22 80 41 aact:AA01457|3end_D-xylose_ABC_transporter,_membrane_spanning_protein_978808..978958_POSITIVE 410 80 48 69 30 aact:AA01985|3end_pyruvate_dehydrogenase,_E1_component_1348801..1348951_POSITIVE 394 69 29 87 51 aact:AA02671|3end_gluconokinase_1858917..1859067_POSITIVE 373 94 51 75 29 aact:AA00363|3end_50S_ribosomal_protein_L22_245980..246130_POSITIVE 371 63 28 151 110 aact:AA00267|3end_hypothetical_protein_188143..188293_POSITIVE 370 80 36 56 17 aact:AA00399|3end_conserved_hypothetical_protein_268363..268513_POSITIVE 368 85 45 59 11 aact:AA00592|3end_conserved_hypothetical_protein_(membrane/transport_protein)_407286..407436_POSITIVE 365 60 14 56 18 aact:AA00112|3end_uracil_permease_81239..81389_POSITIVE 363 80 41 60 15 aact:AA00985|3end_transcriptional_regulator_(LysR_family)_689741..689891_POSITIVE 361 80 36 56 11 aact:AA01023|3end_conserved_hypothetical_protein_716435..716585_POSITIVE 357 80 32 53 4 aact:AA02962|3end_recombination_associated_protein_2072285..2072435_POSITIVE 356 77 41 93 57 aact:AA01459|3end_Na(+)/H(+)_antiporter_981492..981642_POSITIVE 355 80 35 151 107 aact:AA00408|3end_SUN_protein_(FMU_protein)_273688..273838_POSITIVE