Origin IGS: taaaggcaataagcgtatattggtgaatggataacggcacttgagcagagatatatctgtttcaagtgccgttcgtttattggtaagttcttcgtttaatcatttttcta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagaaaaatgattaaacgaagaacttaccaataaacgaacggcacttgaaacagatatatctctgctcaagtgccgttatccattcaccaatatacgcttattgccttta Mask Tandem Repeat Region ================================================ taaaggcaataagcgtatattggtgaatggataacggcacttgagcagagatatatctgtttcaagtgccgttcgtttattggtaagttcttcgtttaatcatttttcta Find is-nt database================================================ Query_seq: PI0380:PI0381|PI0380:PI0381:conserved hypothetical protein:probable transcriptional regulator, AraC family:->->:350602..350711 110 taaaggcaataagcgtatattggtgaatggataacggcacttgagcagagatatatctgtttcaagtgccgttcgtttattggtaagttcttcgtttaatcatttttcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0380:PI0381|PI0380:PI0381:conserved hypothetical protein:probable transcriptional regulator, AraC family:->->:350602..350711 110 taaaggcaataagcgtatattggtgaatggataacggcacttgagcagagatatatctgtttcaagtgccgttcgtttattggtaagttcttcgtttaatcatttttcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0380:PI0381|PI0380:PI0381:conserved hypothetical protein:probable transcriptional regulator, AraC family:->->:350602..350711 110 taaaggcaataagcgtatattggtgaatggataacggcacttgagcagagatatatctgtttcaagtgccgttcgtttattggtaagttcttcgtttaatcatttttcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaggcaataagcgtatattggtgaatggataacggcacttgagcagagatatatctgtttcaagtgccgttcgtttattggtaagttcttcgtttaatcatttttcta Predict ORF larger than 30AA ================================================ taaaggcaataagcgtatattggtgaatggataacggcacttgagcagagatatatctgtttcaagtgccgttcgtttattggtaagttcttcgtttaatcatttttcta 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================================================ taaaggcaataagcgtatattggtgaatggataacggcacttgagcagagatatatctgtttcaagtgccgttcgtttattggtaagttcttcgtttaatcatttttcta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 76 HP_score: -7.3 Tail_Score: -4.26871 Start: 31 End: 75 Full_Region: TATATTGGTGAATGG ATAACGGCACTTGAGCAGA GATATA TCTGTTTCAAGTGCCGTTCG TTTATTGGTAAGTTC ..............................ATAACGGCACTTGAGCAGAGATATATCTGTTTCAAGTGCCGTTCG................................... TransTerm Strand: + Conf: 95 HP_score: -12.5 Tail_Score: -3.70925 Start: 35 End: 71 Full_Region: TTGGTGAATGGATAA CGGCACTTGAGCAGA GATATA TCTGTTTCAAGTGCCG TTCGTTTATTGGTAA ..................................CGGCACTTGAGCAGAGATATATCTGTTTCAAGTGCCG....................................... TransTerm Strand: - Conf: 81 HP_score: -10.3 Tail_Score: -3.41878 Start: 35 End: 71 Full_Region: ttaccaataaacgaa cggcacttgaaacaga tatatc tctgctcaagtgccg ttatccattcaccaa ..................................cggcacttgaaacagatatatctctgctcaagtgccg....................................... Find igs database================================================ Query_seq: PI0380:PI0381|PI0380:PI0381:conserved hypothetical protein:probable transcriptional regulator, AraC family:->->:350602..350711 110 taaaggcaataagcgtatattggtgaatggataacggcacttgagcagagatatatctgtttcaagtgccgttcgtttattggtaagttcttcgtttaatcatttttcta Intra-Species Hit: Count: 1 Min: 1 Max: 110 Len: 110 Subject: pint_PI0380_PI0381|conserved hypothetical protein:probable transcriptional regulator, AraC family|POSITIVE:POSITIVE|[350602,350711]|110 HSP 1 e-value: 3.0E-56 bit: 218.0 Len: 110 Query Start:1 Query End:110 Subject Strand: POSITIVE Subject Start: 1 Subject End: 110 taaaggcaataagcgtatattggtgaatggataacggcacttgagcagagatatatctgtttcaagtgccgttcgtttattggtaagttcttcgtttaatcatttttcta taaaggcaataagcgtatattggtgaatggataacggcacttgagcagagatatatctgtttcaagtgccgttcgtttattggtaagttcttcgtttaatcatttttcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGGCAAUAAGCGUAUAUUGGUGAAUGGAUAACGGCACUUGAGCAGAGAUAUAUCUGUUUCAAGUGCCGUUCGUUUAUUGGUAAGUUCUUCGUUUAAUCAUUUUUCUA .........((((((..(((..((((((((...((((((((((((((((......)))).))))))))))))))))))))..))).......))))))............ (-38.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAAAAAUGAUUAAACGAAGAACUUACCAAUAAACGAACGGCACUUGAAACAGAUAUAUCUCUGCUCAAGUGCCGUUAUCCAUUCACCAAUAUACGCUUAUUGCCUUUA .................((((................((((((((((((..((((......)))).))))))))))))..........(((((......))))).)))). (-26.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 338 49 3 119 71 pint:PI0719|5end_conserved_hypothetical_protein_653043..653273_POSITIVE 324 70 21 170 122 pint:PI1135|5end_hypothetical_protein_1061935..1062165_POSITIVE 310 48 3 155 102 pint:PI1081|5end_probable_endonuclease/resolvase_1000806..1001036_POSITIVE 308 46 5 108 68 pint:PI0605|5end_chloromuconate_cycloisomerase_551912..552142_POSITIVE 296 48 5 52 14 pint:PI0628|5end_phosphoribosylglycinamide_formyltransferase_576027..576257_POSITIVE 293 60 11 160 94 pint:PI0715|5end_hypothetical_protein_652311..652541_POSITIVE 288 49 5 166 123 pint:PI0171|5end_hypothetical_protein_163850..164080_POSITIVE 287 49 5 144 100 pint:PI1547|5end_hypothetical_protein_1465808..1466038_POSITIVE 275 48 2 77 14 pint:PI1378|5end_GTP-binding_protein_lepA_1299904..1300134_POSITIVE 273 94 56 68 39 pint:PI1747|5end_membrane-bound_lytic_murein_transglycosylase_D_1667483..1667713_POSITIVE 273 70 30 81 36 pint:PI0550|5end_possible_glycosyl_hydrolase_500650..500880_POSITIVE 269 99 56 99 52 pint:PI0220|5end_conserved_hypothetical_protein_211980..212210_POSITIVE 265 59 11 72 18 pint:PI1923|5end_conserved_hypothetical_protein_1865560..1865790_POSITIVE 265 48 4 138 86 pint:PI0769|5end_phosphomannomutase_704653..704883_POSITIVE 264 103 61 91 45 pint:PI1862|5end_hypothetical_protein_1806189..1806419_POSITIVE 263 105 61 199 147 pint:PI1382|5end_hypothetical_protein_1303608..1303838_POSITIVE 262 60 12 160 122 pint:PI0533|5end_ABC_transporter,_permease_protein_487259..487489_POSITIVE 262 79 35 106 58 pint:PI0250|5end_hypothetical_protein_246946..247176_POSITIVE 261 49 1 65 4 pint:PI1858|5end_conserved_hypothetical_protein_1804400..1804630_POSITIVE 260 77 35 104 49 pint:PI1896|5end_hypothetical_protein_1840854..1841084_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 524 79 33 67 18 pint:PI0380|3end_conserved_hypothetical_protein_350541..350691_POSITIVE 417 49 4 128 69 pint:PI0056|3end_conserved_hypothetical_protein;_possible_DNA_uptake_protein_55907..56057_POSITIVE 338 49 3 116 68 pint:PI0717|3end_conserved_hypothetical_protein_653120..653270_POSITIVE 288 49 5 127 84 pint:PI0170|3end_hypothetical_protein_163891..164041_POSITIVE 281 47 3 151 99 pint:PI1080|3end_conserved_hypothetical_protein;_possible_outer_membrane_lipoprotein_1000883..1001033_POSITIVE 273 94 56 111 82 pint:PI1746|3end_hypothetical_protein_1667606..1667756_POSITIVE 269 99 56 76 29 pint:PI0219|3end_conserved_hypothetical_protein_212037..212187_POSITIVE 268 57 18 122 86 pint:PI0510|3end_hypothetical_protein_470299..470449_POSITIVE 265 48 4 66 14 pint:PI0768|3end_conserved_hypothetical_protein;_possible_acetyltransferase_704661..704811_POSITIVE 264 103 61 81 35 pint:PI1860|3end_hypothetical_protein_1806259..1806409_POSITIVE 263 75 34 46 3 pint:PI0549|3end_hypothetical_protein_500691..500841_POSITIVE 262 60 12 150 112 pint:PI0532|3end_ABC_transporter,_ATP-binding/permease_protein_487329..487479_POSITIVE 262 79 35 106 58 pint:PI0249|3end_conserved_hypothetical_protein_247026..247176_POSITIVE 255 73 31 83 41 pint:PI0536|3end_hypothetical_protein_492623..492773_POSITIVE 252 43 5 133 93 pint:PI0807|3end_hydrolase,_haloacid_dehalogenase-like_hydrolase_745278..745428_POSITIVE 251 78 36 83 32 pint:PI0570|3end_exsB_protein;_possible_aluminum_resistance_protein_515395..515545_POSITIVE 249 47 2 124 67 pint:PI0312|3end_hypothetical_protein_294940..295090_POSITIVE 248 59 13 81 24 pint:PI1639|3end_conserved_hypothetical_protein_1558133..1558283_POSITIVE 246 50 2 105 53 pint:PI1470|3end_hypothetical_protein_1395122..1395272_POSITIVE 245 78 35 92 50 pint:PI0787|3end_glycosyltransferase_725793..725943_POSITIVE