Origin IGS: tgttattccgtaaaaataccgaaaaaaatgaccgcactttgaggtgctcggtgagcgaaaagtgcggtcgtttttgaaaacgttttaagccgccgttatcatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatgataacggcggcttaaaacgttttcaaaaacgaccgcacttttcgctcaccgagcacctcaaagtgcggtcatttttttcggtatttttacggaataaca Mask Tandem Repeat Region ================================================ tgttattccgtaaaaataccgaaaaaaatgaccgcactttgaggtgctcggtgagcgaaaagtgcggtcgtttttgaaaacgttttaagccgccgttatcatta Find is-nt database================================================ Query_seq: AA02409:AA02410|AA02409:AA02410:DNA ligase:cell division protein:->->:1655465..1655568 104 tgttattccgtaaaaataccgaaaaaaatgaccgcactttgaggtgctcggtgagcgaaaagtgcggtcgtttttgaaaacgttttaagccgccgttatcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA02409:AA02410|AA02409:AA02410:DNA ligase:cell division protein:->->:1655465..1655568 104 tgttattccgtaaaaataccgaaaaaaatgaccgcactttgaggtgctcggtgagcgaaaagtgcggtcgtttttgaaaacgttttaagccgccgttatcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA02409:AA02410|AA02409:AA02410:DNA ligase:cell division protein:->->:1655465..1655568 104 tgttattccgtaaaaataccgaaaaaaatgaccgcactttgaggtgctcggtgagcgaaaagtgcggtcgtttttgaaaacgttttaagccgccgttatcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgttattccgtaaaaataccgaaaaaaatgaccgcactttgaggtgctcggtgagcgaaaagtgcggtcgtttttgaaaacgttttaagccgccgttatcatta Predict ORF larger than 30AA ================================================ tgttattccgtaaaaataccgaaaaaaatgaccgcactttgaggtgctcggtgagcgaaaagtgcggtcgtttttgaaaacgttttaagccgccgttatcatta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 87 Start: 73 End: 102 ........................................................................TTTGAAAACGTTTTAAGCCGCCGTTATCAT.. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgttattccgtaaaaataccgaaaaaaatgaccgcactttgaggtgctcggtgagcgaaaagtgcggtcgtttttgaaaacgttttaagccgccgttatcatta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 59 HP_score: -5.0 Tail_Score: -3.90118 Start: 30 End: 69 Full_Region: aacgttttcaaaaac gaccgcacttttcgct caccgagc acctcaaagtgcggtc atttttttcggtatt .............................gaccgcacttttcgctcaccgagcacctcaaagtgcggtc................................... Find igs database================================================ Query_seq: AA02409:AA02410|AA02409:AA02410:DNA ligase:cell division protein:->->:1655465..1655568 104 tgttattccgtaaaaataccgaaaaaaatgaccgcactttgaggtgctcggtgagcgaaaagtgcggtcgtttttgaaaacgttttaagccgccgttatcatta Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: aact_AA02409_AA02410|DNA ligase:cell division protein|POSITIVE:POSITIVE|[1655465,1655568]|104 HSP 1 e-value: 3.0E-40 bit: 165.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 tgttattccgtaaaaataccgnnnnnnntgaccgcactttgaggtgctcggtgagcgaaaagtgcggtcgtttttgaaaacgttttaagccgccgttatcatta tgttattccgtaaaaataccgaaaaaaatgaccgcactttgaggtgctcggtgagcgaaaagtgcggtcgtttttgaaaacgttttaagccgccgttatcatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUAUUCCGUAAAAAUACCGAAAAAAAUGACCGCACUUUGAGGUGCUCGGUGAGCGAAAAGUGCGGUCGUUUUUGAAAACGUUUUAAGCCGCCGUUAUCAUUA .....(((.(((....))).))).((((((((((((((((....(((((...))))).))))))))))))))))(((.((((...........)))).)))... (-32.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGAUAACGGCGGCUUAAAACGUUUUCAAAAACGACCGCACUUUUCGCUCACCGAGCACCUCAAAGUGCGGUCAUUUUUUUCGGUAUUUUUACGGAAUAACA ...(((.((((...........)))).))).....(((((((((((..((((...)))).....)))))))))))......(((.(((....))).)))..... (-30.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 574 70 21 148 103 aact:AA00613|5end_lipid-A-disaccharide_synthase_418713..418943_POSITIVE 528 69 21 149 106 aact:AA01692|5end_hexulose-6-phosphate_synthase_1149178..1149408_POSITIVE 527 60 11 155 107 aact:AA01027|5end_Na(+)-translocating_NADH-quinone_reductase_subunit_F_717676..717906_POSITIVE 519 70 21 153 110 aact:AA00511|5end_nicotinamide_mononucleotide_transporter_353884..354114_POSITIVE 498 67 22 156 115 aact:AA00464|5end_conserved_hypothetical_protein_323912..324142_POSITIVE 487 70 23 147 105 aact:AA01704|5end_tyrosine-specific_transport_protein_1156170..1156400_POSITIVE 485 70 26 161 124 aact:AA01519|5end_conserved_hypothetical_protein_1021794..1022024_POSITIVE 481 69 21 152 114 aact:AA02963|5end_opacity_associated_protein_B_2072302..2072532_POSITIVE 479 74 31 200 161 aact:AA02486|5end_topoisomerase_IV,_subunit_B_1724337..1724567_POSITIVE 477 75 31 158 117 aact:AA01436|5end_fructose-bisphosphate_aldolase_class_II_962981..963211_POSITIVE 476 74 32 231 173 aact:AA00770|5end_outer_membrane_protein_precursor_530788..531018_POSITIVE 474 49 7 148 102 aact:AA02131|5end_conserved_hypothetical_protein_(possible_TrpH_protein)_1454239..1454469_POSITIVE 466 90 43 67 16 aact:AA00582|5end_conserved_hypothetical_protein_397904..398134_POSITIVE 459 67 27 162 123 aact:AA00419|5end_conserved_hypothetical_protein_(possible_phosphatidylethanolamine-binding_protein)_284337..284567_POSITIVE 452 75 32 115 66 aact:AA00835|5end_UDP-N-acetylglucosamine-N-acetylmuramyl-(pentapep_tide)_575212..575442_POSITIVE 450 78 31 146 103 aact:AA00047|5end_formate_dependent_nitrite_reductase,_cytochrome_c552_36753..36983_POSITIVE 448 42 8 134 97 aact:AA00075|5end_conserved_hypothetical_protein_54963..55193_POSITIVE 446 68 24 146 106 aact:AA02937|5end_conserved_hypothetical_protein_2056379..2056609_POSITIVE 446 69 25 146 107 aact:AA01603|5end_oligopeptidase_A_1082898..1083128_POSITIVE 446 87 43 210 156 aact:AA01284|5end_heat_shock_protein_(hsp60)_868574..868804_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 574 70 21 60 15 aact:AA00612|3end_acyl-(acyl-carrier-protein)-UDP-N-acetylglucosami_ne_418705..418855_POSITIVE 519 70 21 72 29 aact:AA00508|3end_SAM-dependent_methyltransferase_353883..354033_POSITIVE 498 67 22 62 21 aact:AA00463|3end_class_B_acid_phosphatase_323898..324048_POSITIVE 487 70 23 58 16 aact:AA01703|3end_L-ribulose-phosphate_4-epimerase_1156161..1156311_POSITIVE 485 70 26 78 41 aact:AA01517|3end_peptidyl-prolyl_cis-trans_isomerase;_macrophage_infectivity_protein_1021791..1021941_POSITIVE 481 69 21 55 17 aact:AA02962|3end_recombination_associated_protein_2072285..2072435_POSITIVE 477 75 31 118 77 aact:AA01434|3end_conserved_hypothetical_protein_(possible_o-antigen_ligase)_963021..963171_POSITIVE 474 49 7 130 84 aact:AA02130|3end_hypothetical_protein_1454301..1454451_POSITIVE 463 69 24 61 16 aact:AA02409|3end_DNA_ligase_1655404..1655554_POSITIVE 459 67 27 53 14 aact:AA00417|3end_outer_membrane_lipoprotein_precursor_(probable_D-methionine-binding_lipoprotein)_284308..284458_POSITIVE 450 78 31 69 26 aact:AA00046|3end_formate_dependent_nitrite_reductase,_cytochrome-c_type_protein_36756..36906_POSITIVE 448 42 8 38 1 aact:AA00072|3end_conserved_hypothetical_protein_54947..55097_POSITIVE 446 68 24 60 20 aact:AA02936|3end_lipoprotein_E_precursor;_outer_membrane_protein_P4_precursor;_acid_phosphatase_2056373..2056523_POSITIVE 446 87 43 86 32 aact:AA01280|3end_groES_chaperonin_868530..868680_POSITIVE 439 70 28 151 100 aact:AA00271|3end_hypothetical_protein_190469..190619_POSITIVE 436 75 39 41 1 aact:AA00833|3end_UDP-N-acetylmuramate-alanine_ligase_575218..575368_POSITIVE 427 78 31 73 30 aact:AA00974|3end_glucosamine-fructose-6-phosphate_681127..681277_POSITIVE 423 75 31 107 67 aact:AA02135|3end_hypothetical_protein_1459067..1459217_POSITIVE 423 75 31 123 83 aact:AA02135.1|3end_hypothetical_protein_1459083..1459233_POSITIVE 422 100 52 114 63 aact:AA01172|3end_conserved_hypothetical_protein_803847..803997_POSITIVE