Origin IGS: tatgatgttacctcaaattgatgcactcggcgaatgctcacaccgaacacgttattaatagaaaataagacgacgaattataacgggacaaaggctttccgtcgaggaaatgcacgataaaagcgcataattgattaaaaaacactcgatttattccataaaatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taattttatggaataaatcgagtgttttttaatcaattatgcgcttttatcgtgcatttcctcgacggaaagcctttgtcccgttataattcgtcgtcttattttctattaataacgtgttcggtgtgagcattcgccgagtgcatcaatttgaggtaacatcata Mask Tandem Repeat Region ================================================ tatgatgttacctcaaattgatgcactcggcgaatgctcacaccgaacacgttattaatagaaaataagacgacgaattataacgggacaaaggctttccgtcgaggaaatgcacgataaaagcgcataattgattaaaaaacactcgatttattccataaaatta Find is-nt database================================================ Query_seq: AA02955:AA02956|AA02955:AA02956:trigger factor:integrase-recombinase:->->:2068458..2068623 166 tatgatgttacctcaaattgatgcactcggcgaatgctcacaccgaacacgttattaatagaaaataagacgacgaattataacgggacaaaggctttccgtcgaggaaatgcacgataaaagcgcataattgattaaaaaacactcgatttattccataaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA02955:AA02956|AA02955:AA02956:trigger factor:integrase-recombinase:->->:2068458..2068623 166 tatgatgttacctcaaattgatgcactcggcgaatgctcacaccgaacacgttattaatagaaaataagacgacgaattataacgggacaaaggctttccgtcgaggaaatgcacgataaaagcgcataattgattaaaaaacactcgatttattccataaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA02955:AA02956|AA02955:AA02956:trigger factor:integrase-recombinase:->->:2068458..2068623 166 tatgatgttacctcaaattgatgcactcggcgaatgctcacaccgaacacgttattaatagaaaataagacgacgaattataacgggacaaaggctttccgtcgaggaaatgcacgataaaagcgcataattgattaaaaaacactcgatttattccataaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatgatgttacctcaaattgatgcactcggcgaatgctcacaccgaacacgttattaatagaaaataagacgacgaattataacgggacaaaggctttccgtcgaggaaatgcacgataaaagcgcataattgattaaaaaacactcgatttattccataaaatta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 58 End: 150 ......................................................... Y F I L R R I I V P C L S E T S S I C S L L A Y N I L F C E M ................ Protein_Len: 38 Strand: - Start: 41 End: 154 ........................................ V S C T I L L F Y S S S N Y R S L P K G D L F H V I F A C L Q N F F V R N M ............ tatgatgttacctcaaattgatgcactcggcgaatgctcacaccgaacacgttattaatagaaaataagacgacgaattataacgggacaaaggctttccgtcgaggaaatgcacgataaaagcgcataattgattaaaaaacactcgatttattccataaaatta 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: 85 Start: 77 End: 106 ............................................................................CTCGACGGAAAGCCTTTGTCCCGTTATAAT............................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tatgatgttacctcaaattgatgcactcggcgaatgctcacaccgaacacgttattaatagaaaataagacgacgaattataacgggacaaaggctttccgtcgaggaaatgcacgataaaagcgcataattgattaaaaaacactcgatttattccataaaatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA02955:AA02956|AA02955:AA02956:trigger factor:integrase-recombinase:->->:2068458..2068623 166 tatgatgttacctcaaattgatgcactcggcgaatgctcacaccgaacacgttattaatagaaaataagacgacgaattataacgggacaaaggctttccgtcgaggaaatgcacgataaaagcgcataattgattaaaaaacactcgatttattccataaaatta Intra-Species Hit: Count: 1 Min: 1 Max: 166 Len: 166 Subject: aact_AA02955_AA02956|trigger factor:integrase-recombinase|POSITIVE:POSITIVE|[2068458, 2068623]|166 HSP 1 e-value: 2.0E-89 bit: 329.0 Len: 166 Query Start:1 Query End:166 Subject Strand: POSITIVE Subject Start: 1 Subject End: 166 tatgatgttacctcaaattgatgcactcggcgaatgctcacaccgaacacgttattaatagaaaataagacgacgaattataacgggacaaaggctttccgtcgaggaaatgcacgataaaagcgcataattgattaaaaaacactcgatttattccataaaatta tatgatgttacctcaaattgatgcactcggcgaatgctcacaccgaacacgttattaatagaaaataagacgacgaattataacgggacaaaggctttccgtcgaggaaatgcacgataaaagcgcataattgattaaaaaacactcgatttattccataaaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUGAUGUUACCUCAAAUUGAUGCACUCGGCGAAUGCUCACACCGAACACGUUAUUAAUAGAAAAUAAGACGACGAAUUAUAACGGGACAAAGGCUUUCCGUCGAGGAAAUGCACGAUAAAAGCGCAUAAUUGAUUAAAAAACACUCGAUUUAUUCCAUAAAAUUA ..............(((((((((..(((((((((.(((....(((....(((..((............))..)))........)))......))).)).)))))))...((((.(.......).))))..............)).))))))).............. (-24.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUUUAUGGAAUAAAUCGAGUGUUUUUUAAUCAAUUAUGCGCUUUUAUCGUGCAUUUCCUCGACGGAAAGCCUUUGUCCCGUUAUAAUUCGUCGUCUUAUUUUCUAUUAAUAACGUGUUCGGUGUGAGCAUUCGCCGAGUGCAUCAAUUUGAGGUAACAUCAUA ......(((((..((..((((((.....(((((.....((((((.......)))))).....(((((((....................)))))))...........)))))....(..(((((((........)))))))..)....))))))..))...))))) (-31.45) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 373 119 72 170 125 aact:AA00469|5end_inorganic_pyrophosphatase,_chain_A_326206..326436_POSITIVE 317 120 84 51 9 aact:AA00204|5end_(di)nucleoside_polyphosphate_hydrolase;_possible_invasion_protein_141346..141576_POSITIVE 308 117 71 207 144 aact:AA01675|5end_probable_multidrug_resistance_protein;_multidrug-efflux_transporter_1132115..1132345_POSITIVE 308 117 71 109 46 aact:AA01674|5end_hypothetical_protein_1132017..1132247_POSITIVE 305 52 11 73 35 aact:AA02146|5end_iron(III)_ABC_transporter,_ATP-binding_protein_1468828..1469058_POSITIVE 301 114 72 195 138 aact:AA02575|5end_transmembrane_protein_1793749..1793979_POSITIVE 299 127 82 178 136 aact:AA01745|5end_conserved_hypothetical_protein_(possible_peptide_chain_release_factor_2)_1180394..1180624_POSITIVE 298 126 84 230 197 aact:AA00046|5end_formate_dependent_nitrite_reductase,_cytochrome-c_type_protein_36014..36244_POSITIVE 296 118 71 58 14 aact:AA01066|5end_conserved_hypothetical_protein_738380..738610_POSITIVE 293 52 11 69 25 aact:AA00990|5end_conserved_hypothetical_protein_692559..692789_POSITIVE 287 45 10 42 3 aact:AA00715|5end_[2Fe-2S]_ferredoxin_490632..490862_POSITIVE 285 54 12 77 33 aact:AA00488|5end_purine_nucleoside_phosphorylase_338075..338305_POSITIVE 283 117 71 58 8 aact:AA01477|5end_type_I_restriction_enzyme_R_protein_992249..992479_POSITIVE 282 124 84 224 186 aact:AA00537|5end_conserved_hypothetical_protein_367992..368222_POSITIVE 282 45 4 51 8 aact:AA00214|5end_glutamyl-tRNA_synthetase_147727..147957_POSITIVE 280 127 81 188 136 aact:AA02367|5end_conserved_hypothetical_protein_1623174..1623404_POSITIVE 280 120 71 61 4 aact:AA00579|5end_probable_DNA_recombination_protein_395265..395495_POSITIVE 279 113 74 114 75 aact:AA00142|5end_glycerate_kinase_101309..101539_POSITIVE 277 116 72 65 12 aact:AA00207|5end_D-ribose_ABC_transporter,_ATP-binding_protein_/_galactoside_ABC_transporter,_ATP-binding_protein_142592..142822_POSITIVE 275 128 89 69 25 aact:AA02936|5end_lipoprotein_E_precursor;_outer_membrane_protein_P4_precursor;_acid_phosphatase_2055610..2055840_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 320 120 71 147 108 aact:AA00585|3end_glycerol-3-phosphate_regulon_repressor_399778..399928_POSITIVE 317 120 84 45 3 aact:AA00202|3end_conserved_hypothetical_protein_(possible_membrane_protein)_141420..141570_POSITIVE 308 117 71 105 42 aact:AA01673|3end_riboflavin_synthase,_alpha_chain_1132093..1132243_POSITIVE 299 127 82 56 14 aact:AA01744|3end_peptide_chain_release_factor_RF-2_1180352..1180502_POSITIVE 293 52 11 74 30 aact:AA00989|3end_hypothetical_protein_692644..692794_POSITIVE 276 126 90 147 105 aact:AA01476|3end_hypothetical_protein_992261..992411_POSITIVE 273 53 11 77 35 aact:AA00573|3end_chloramphenicol-sensitive_protein_RarD_393295..393445_POSITIVE 272 135 96 140 100 aact:AA00398|3end_protein-tyrosine-phosphatase_(PTPase)_268018..268168_POSITIVE 270 127 87 60 14 aact:AA02005|3end_vancomycin_sensitivity;_SanA_protein_1364020..1364170_POSITIVE 269 125 84 44 1 aact:AA00241|3end_formate_acetyltransferase_activating_enzyme_(anaerobic_ribonucleoside-triphosphate_reductase_activating_protein)_172090..172240_POSITIVE 266 116 84 51 5 aact:AA00205|3end_ribose_ABC_transporter_protein_/_high_affinity_D-ribose_transport_protein_142658..142808_POSITIVE 266 113 78 38 1 aact:AA00141|3end_hypoxanthine_phosphoribosyl_transferase_(HPRT)_101313..101463_POSITIVE 263 69 25 61 2 aact:AA00140|3end_hypothetical_protein_100872..101022_POSITIVE 262 47 3 133 89 aact:AA01286|3end_5,10-methylenetetrahydrofolate_dehydrogenase_(bifunctional_protein)_871243..871393_POSITIVE 261 61 21 71 22 aact:AA01235|3end_30S_ribosomal_protein_S5_842346..842496_POSITIVE 258 64 30 26 1 aact:AA01358|3end_conserved_hypothetical_protein_920387..920537_POSITIVE 258 68 27 85 37 aact:AA01156|3end_chaperonin_heat_shock_protein_33_homolog_792408..792558_POSITIVE 256 132 94 148 99 aact:AA01859|3end_hypothetical_protein_1251890..1252040_POSITIVE 255 130 84 98 50 aact:AA02369|3end_conserved_hypothetical_protein_1624648..1624798_POSITIVE 255 128 84 79 35 aact:AA01269|3end_hypothetical_protein_863413..863563_POSITIVE