Origin IGS: tagggggaaaataaggaagatgggaagcgataaactttaaaattcactgtaaaaatagaccgcacttggcgttgctcgatcaaagtgcggtcatttttttcggtgtttttaatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taattaaaaacaccgaaaaaaatgaccgcactttgatcgagcaacgccaagtgcggtctatttttacagtgaattttaaagtttatcgcttcccatcttccttattttcccccta Mask Tandem Repeat Region ================================================ tagggggaaaataaggaagatgggaagcgataaactttaaaattcactgtaaaaatagaccgcacttggcgttgctcgatcaaagtgcggtcatttttttcggtgtttttaatta Find is-nt database================================================ Query_seq: AA01690:AA01692|AA01690:AA01692:penicillin-binding protein 1C:hexulose-6-phosphate synthase:->->:1149203..1149317 115 tagggggaaaataaggaagatgggaagcgataaactttaaaattcactgtaaaaatagaccgcacttggcgttgctcgatcaaagtgcggtcatttttttcggtgtttttaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01690:AA01692|AA01690:AA01692:penicillin-binding protein 1C:hexulose-6-phosphate synthase:->->:1149203..1149317 115 tagggggaaaataaggaagatgggaagcgataaactttaaaattcactgtaaaaatagaccgcacttggcgttgctcgatcaaagtgcggtcatttttttcggtgtttttaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01690:AA01692|AA01690:AA01692:penicillin-binding protein 1C:hexulose-6-phosphate synthase:->->:1149203..1149317 115 tagggggaaaataaggaagatgggaagcgataaactttaaaattcactgtaaaaatagaccgcacttggcgttgctcgatcaaagtgcggtcatttttttcggtgtttttaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagggggaaaataaggaagatgggaagcgataaactttaaaattcactgtaaaaatagaccgcacttggcgttgctcgatcaaagtgcggtcatttttttcggtgtttttaatta Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: - Start: 3 End: 113 .. P S F L S S P F R Y V K F N V T F I S R V Q R Q E I L T R D N K E T N K M .. tagggggaaaataaggaagatgggaagcgataaactttaaaattcactgtaaaaatagaccgcacttggcgttgctcgatcaaagtgcggtcatttttttcggtgtttttaatta 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================================================ tagggggaaaataaggaagatgggaagcgataaactttaaaattcactgtaaaaatagaccgcacttggcgttgctcgatcaaagtgcggtcatttttttcggtgtttttaatta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 87 HP_score: -4.5 Tail_Score: -5.54264 Start: 57 End: 93 Full_Region: ATTCACTGTAAAAAT AGACCGCACTTGGCG TTGCT CGATCAAAGTGCGGTCA TTTTTTTCGGTGTTT ........................................................AGACCGCACTTGGCGTTGCTCGATCAAAGTGCGGTCA...................... TransTerm Strand: + Conf: 72 HP_score: -8.0 Tail_Score: -3.90118 Start: 58 End: 92 Full_Region: TTCACTGTAAAAATA GACCGCACTTGGCG TTGCT CGATCAAAGTGCGGTC ATTTTTTTCGGTGTT .........................................................GACCGCACTTGGCGTTGCTCGATCAAAGTGCGGTC....................... Find igs database================================================ Query_seq: AA01690:AA01692|AA01690:AA01692:penicillin-binding protein 1C:hexulose-6-phosphate synthase:->->:1149203..1149317 115 tagggggaaaataaggaagatgggaagcgataaactttaaaattcactgtaaaaatagaccgcacttggcgttgctcgatcaaagtgcggtcatttttttcggtgtttttaatta Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: aact_AA01690_AA01692|penicillin-binding protein 1C:hexulose-6-phosphate synthase|POSITIVE:POSITIVE|[1149203,1149317]|115 HSP 1 e-value: 1.0E-46 bit: 186.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 tagggggaaaataaggaagatgggaagcgataaactttaaaattcactgtaaaaatagaccgcacttggcgttgctcgatcaaagtgcggtcannnnnnncggtgtttttaatta tagggggaaaataaggaagatgggaagcgataaactttaaaattcactgtaaaaatagaccgcacttggcgttgctcgatcaaagtgcggtcatttttttcggtgtttttaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGGGGAAAAUAAGGAAGAUGGGAAGCGAUAAACUUUAAAAUUCACUGUAAAAAUAGACCGCACUUGGCGUUGCUCGAUCAAAGUGCGGUCAUUUUUUUCGGUGUUUUUAAUUA ...........(((((...((.(....).))...)))))(((..(((((.((((((.((((((((((((((.....)).)).))))))))))))))))..)))))..)))..... (-31.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUAAAAACACCGAAAAAAAUGACCGCACUUUGAUCGAGCAACGCCAAGUGCGGUCUAUUUUUACAGUGAAUUUUAAAGUUUAUCGCUUCCCAUCUUCCUUAUUUUCCCCCUA ...((((((.(((.(.(((((..((((((((((....((.....))..))))))))))..))))).).)))..)))))).................................... (-21.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 596 110 61 184 130 aact:AA02410|5end_cell_division_protein_1655429..1655659_POSITIVE 529 109 61 169 122 aact:AA00511|5end_nicotinamide_mononucleotide_transporter_353884..354114_POSITIVE 522 100 51 160 109 aact:AA01436|5end_fructose-bisphosphate_aldolase_class_II_962981..963211_POSITIVE 505 90 41 144 95 aact:AA00987|5end_tetracenomycin_polyketide_synthesis_O-methyltransferase_689745..689975_POSITIVE 485 109 69 212 174 aact:AA02246|5end_peptidase_E_1527574..1527804_POSITIVE 485 109 69 84 46 aact:AA02245|5end_hypothetical_protein_1527446..1527676_POSITIVE 479 109 61 63 10 aact:AA00582|5end_conserved_hypothetical_protein_397904..398134_POSITIVE 476 97 51 229 181 aact:AA00976|5end_conserved_hypothetical_protein_681206..681436_POSITIVE 465 90 41 156 105 aact:AA00464|5end_conserved_hypothetical_protein_323912..324142_POSITIVE 453 92 51 147 105 aact:AA00613|5end_lipid-A-disaccharide_synthase_418713..418943_POSITIVE 450 110 61 127 73 aact:AA01059|5end_orotate_phosphoribosyltransferase_735052..735282_POSITIVE 440 109 61 187 132 aact:AA02162|5end_lipoprotein_1478950..1479180_POSITIVE 426 110 65 184 129 aact:AA02915|5end_thioredoxin_m_2040652..2040882_POSITIVE 423 97 58 153 112 aact:AA02937|5end_conserved_hypothetical_protein_2056379..2056609_POSITIVE 418 110 61 121 67 aact:AA00837|5end_cell_division_protein_W_576317..576547_POSITIVE 417 100 51 155 106 aact:AA02252|5end_conserved_hypothetical_protein_1533840..1534070_POSITIVE 415 109 62 171 122 aact:AA03003|5end_GTP-binding_membrane_protein_2096544..2096774_POSITIVE 415 109 62 50 1 aact:AA03002|5end_hypothetical_protein_2096423..2096653_POSITIVE 415 109 63 209 166 aact:AA01284|5end_heat_shock_protein_(hsp60)_868574..868804_POSITIVE 414 90 45 149 113 aact:AA01027|5end_Na(+)-translocating_NADH-quinone_reductase_subunit_F_717676..717906_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 596 110 61 79 25 aact:AA02409|3end_DNA_ligase_1655404..1655554_POSITIVE 529 109 61 88 41 aact:AA00508|3end_SAM-dependent_methyltransferase_353883..354033_POSITIVE 522 100 51 120 69 aact:AA01434|3end_conserved_hypothetical_protein_(possible_o-antigen_ligase)_963021..963171_POSITIVE 511 109 61 117 69 aact:AA02135|3end_hypothetical_protein_1459067..1459217_POSITIVE 511 109 61 133 85 aact:AA02135.1|3end_hypothetical_protein_1459083..1459233_POSITIVE 505 90 41 60 11 aact:AA00985|3end_transcriptional_regulator_(LysR_family)_689741..689891_POSITIVE 476 97 51 70 22 aact:AA00974|3end_glucosamine-fructose-6-phosphate_681127..681277_POSITIVE 466 110 61 78 30 aact:AA00221|3end_NADP-specific_glutamate_dehydrogenase_153865..154015_POSITIVE 465 90 41 62 11 aact:AA00463|3end_class_B_acid_phosphatase_323898..324048_POSITIVE 453 92 51 59 17 aact:AA00612|3end_acyl-(acyl-carrier-protein)-UDP-N-acetylglucosami_ne_418705..418855_POSITIVE 440 109 61 86 31 aact:AA02160|3end_conserved_hypothetical_protein_1478929..1479079_POSITIVE 425 109 69 45 1 aact:AA00581|3end_thiosulfate_sulfurtransferase_(rhodanese)_397966..398116_POSITIVE 424 90 47 65 11 aact:AA00592|3end_conserved_hypothetical_protein_(membrane/transport_protein)_407286..407436_POSITIVE 423 97 58 67 26 aact:AA02936|3end_lipoprotein_E_precursor;_outer_membrane_protein_P4_precursor;_acid_phosphatase_2056373..2056523_POSITIVE 420 109 68 89 52 aact:AA01778|3end_aminopeptidase_A/I;_cytosol_aminopeptidase;_leucyl_aminopeptidase_1199965..1200115_POSITIVE 418 110 61 77 23 aact:AA00835|3end_UDP-N-acetylglucosamine-N-acetylmuramyl-(pentapep_tide)_576353..576503_POSITIVE 417 100 51 78 29 aact:AA02251|3end_biotin_sulfoxide_reductase;_Trimethylamine-N-oxide_reductase_precursor_1533843..1533993_POSITIVE 415 109 63 85 42 aact:AA01280|3end_groES_chaperonin_868530..868680_POSITIVE 412 98 53 83 41 aact:AA01517|3end_peptidyl-prolyl_cis-trans_isomerase;_macrophage_infectivity_protein_1021791..1021941_POSITIVE 410 110 66 88 46 aact:AA01074|3end_diacylglycerol_kinase_745623..745773_POSITIVE