Origin IGS: tttcttgtattatgctatggtgaaagtgccgggtcggtcaattgaccgaaggcggatatttccaccattatattattcctgtttcctaattatttccggttggcgaatgagaacaagtcccacccaaacaaggcactaaattactattttcgggcaaagggaatacgttcgcaatcaaaaaac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gttttttgattgcgaacgtattccctttgcccgaaaatagtaatttagtgccttgtttgggtgggacttgttctcattcgccaaccggaaataattaggaaacaggaataatataatggtggaaatatccgccttcggtcaattgaccgacccggcactttcaccatagcataatacaagaaa Mask Tandem Repeat Region ================================================ tttcttgtattatgctatggtgaaagtgccgggtcggtcaattgaccgaaggcggatatttccaccattatattattcctgtttcctaattatttccggttggcgaatgagaacaagtcccacccaaacaaggcactaaattactattttcgggcaaagggaatacgttcgcaatcaaaaaac Find is-nt database================================================ Query_seq: PG1386:PG1387|PG1386:PG1387:DNA gyrase, A subunit:hypothetical protein:<-<-:1469039..1469221 183 tttcttgtattatgctatggtgaaagtgccgggtcggtcaattgaccgaaggcggatatttccaccattatattattcctgtttcctaattatttccggttggcgaatgagaacaagtcccacccaaacaaggcactaaattactattttcgggcaaagggaatacgttcgcaatcaaaaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1386:PG1387|PG1386:PG1387:DNA gyrase, A subunit:hypothetical protein:<-<-:1469039..1469221 183 tttcttgtattatgctatggtgaaagtgccgggtcggtcaattgaccgaaggcggatatttccaccattatattattcctgtttcctaattatttccggttggcgaatgagaacaagtcccacccaaacaaggcactaaattactattttcgggcaaagggaatacgttcgcaatcaaaaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1386:PG1387|PG1386:PG1387:DNA gyrase, A subunit:hypothetical protein:<-<-:1469039..1469221 183 tttcttgtattatgctatggtgaaagtgccgggtcggtcaattgaccgaaggcggatatttccaccattatattattcctgtttcctaattatttccggttggcgaatgagaacaagtcccacccaaacaaggcactaaattactattttcgggcaaagggaatacgttcgcaatcaaaaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttcttgtattatgctatggtgaaagtgccgggtcggtcaattgaccgaaggcggatatttccaccattatattattcctgtttcctaattatttccggttggcgaatgagaacaagtcccacccaaacaaggcactaaattactattttcgggcaaagggaatacgttcgcaatcaaaaaac Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 5 End: 136 .... M Y Y A M V K V P G R S I D R R R I F P P L Y Y S C F L I I S G W R M R T S P T Q T R H ............................................... Protein_Len: 42 Strand: + Start: 58 End: 183 ......................................................... M S T I I L F L F P N Y F R L A N E N K S H P N K A L N Y Y F R A K G I R S Q S K N Protein_Len: 30 Strand: - Start: 89 End: 178 ........................................................................................ N N G T P S H S C T G G L C P V L N S N E P L P F V N A I M ..... tttcttgtattatgctatggtgaaagtgccgggtcggtcaattgaccgaaggcggatatttccaccattatattattcctgtttcctaattatttccggttggcgaatgagaacaagtcccacccaaacaaggcactaaattactattttcgggcaaagggaatacgttcgcaatcaaaaaac 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================================================ tttcttgtattatgctatggtgaaagtgccgggtcggtcaattgaccgaaggcggatatttccaccattatattattcctgtttcctaattatttccggttggcgaatgagaacaagtcccacccaaacaaggcactaaattactattttcgggcaaagggaatacgttcgcaatcaaaaaac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1386:PG1387|PG1386:PG1387:DNA gyrase, A subunit:hypothetical protein:<-<-:1469039..1469221 183 tttcttgtattatgctatggtgaaagtgccgggtcggtcaattgaccgaaggcggatatttccaccattatattattcctgtttcctaattatttccggttggcgaatgagaacaagtcccacccaaacaaggcactaaattactattttcgggcaaagggaatacgttcgcaatcaaaaaac Intra-Species Hit: Count: 1 Min: 1 Max: 183 Len: 183 Subject: NC_002950_PG1386_PG1387|DNA gyrase, A subunit:hypothetical protein|NEGATIVE:NEGATIVE|[1469039,1469221]|183 HSP 1 e-value: 1.0E-99 bit: 363.0 Len: 183 Query Start:1 Query End:183 Subject Strand: POSITIVE Subject Start: 1 Subject End: 183 tttcttgtattatgctatggtgaaagtgccgggtcggtcaattgaccgaaggcggatatttccaccattatattattcctgtttcctaattatttccggttggcgaatgagaacaagtcccacccaaacaaggcactaaattactattttcgggcaaagggaatacgttcgcaatcaaaaaac tttcttgtattatgctatggtgaaagtgccgggtcggtcaattgaccgaaggcggatatttccaccattatattattcctgtttcctaattatttccggttggcgaatgagaacaagtcccacccaaacaaggcactaaattactattttcgggcaaagggaatacgttcgcaatcaaaaaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUUGUAUUAUGCUAUGGUGAAAGUGCCGGGUCGGUCAAUUGACCGAAGGCGGAUAUUUCCACCAUUAUAUUAUUCCUGUUUCCUAAUUAUUUCCGGUUGGCGAAUGAGAACAAGUCCCACCCAAACAAGGCACUAAAUUACUAUUUUCGGGCAAAGGGAAUACGUUCGCAAUCAAAAAAC ......(((.((((..((((((.((((((((..((((((....))))))...))).))))).)))))))))).))).....................(((((.((((((........((((.((((((..((...........))..))).)))....))))...)))))))))))....... (-44.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUUUUGAUUGCGAACGUAUUCCCUUUGCCCGAAAAUAGUAAUUUAGUGCCUUGUUUGGGUGGGACUUGUUCUCAUUCGCCAACCGGAAAUAAUUAGGAAACAGGAAUAAUAUAAUGGUGGAAAUAUCCGCCUUCGGUCAAUUGACCGACCCGGCACUUUCACCAUAGCAUAAUACAAGAAA ((((((((((((.(((((...((((...(((((((....(((......)))....)))))))))))..)))))...((((.....))))..))))))))))))............(((((((((....(((...((((((....))))))..)))...)))))))))................ (-52.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 997 60 11 151 102 NC_002950:PG1386|5end_DNA_gyrase,_A_subunit_1468948..1469178_NEGATIVE 379 60 14 85 30 NC_002950:PG1241|5end_GTP-binding_protein_LepA_1315613..1315843_POSITIVE 366 68 26 225 174 NC_002950:PG2031|5end_hypothetical_protein_2130339..2130569_POSITIVE 353 53 15 40 7 NC_002950:PG2041|5end_hypothetical_protein_2139966..2140196_NEGATIVE 350 68 27 99 62 NC_002950:PG1577|5end_nicotinate-nucleotide_pyrophosphorylase_1654619..1654849_POSITIVE 345 55 13 70 31 NC_002950:PG1545|5end_superoxide_dismutase,_Fe-Mn_1623500..1623730_POSITIVE 343 54 13 69 16 NC_002950:PG1290|5end_branched-chain_amino_acid_aminotransferase_1368253..1368483_POSITIVE 341 57 11 189 126 NC_002950:PG1870|5end_methlytransferase,_UbiE/COQ5_family_1966527..1966757_NEGATIVE 333 48 1 78 21 NC_002950:PG0205|5end_peptide_chain_release_factor_3_242093..242323_NEGATIVE 331 139 93 58 7 NC_002950:PG2050|5end_hypothetical_protein_2149434..2149664_NEGATIVE 330 55 14 226 180 NC_002950:PG2079|5end_hypothetical_protein_2179366..2179596_NEGATIVE 329 66 26 58 10 NC_002950:PG0553|5end_extracellular_protease,_putative_611189..611419_NEGATIVE 327 66 25 191 145 NC_002950:PG1180|5end_hypothetical_protein_1263615..1263845_NEGATIVE 326 138 94 75 29 NC_002950:PG2054|5end_lipoprotein_PG3_2152014..2152244_NEGATIVE 324 56 12 56 3 NC_002950:PG2006|5end_hypothetical_protein_2094587..2094817_POSITIVE 324 53 18 54 19 NC_002950:PG1829|5end_long-chain-fatty-acid--CoA_ligase,_putative_1922980..1923210_NEGATIVE 323 54 11 225 171 NC_002950:PG1582|5end_batA_protein_1659321..1659551_POSITIVE 322 57 13 73 15 NC_002950:PG1666|5end_efflux_transporter,_MFP_component,_RND_family_1748442..1748672_POSITIVE 320 57 17 148 110 NC_002950:PG0651|5end_HDIG_domain_protein_703622..703852_NEGATIVE 319 62 21 73 38 NC_002950:PG1996|5end_deoxyribose-phosphate_aldolase_2085921..2086151_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 350 68 27 52 15 NC_002950:PG1576|3end_L-aspartate_oxidase_1654652..1654802_POSITIVE 341 57 11 147 84 NC_002950:PG1871|3end_hypothetical_protein_1966569..1966719_NEGATIVE 327 66 25 150 104 NC_002950:PG1181|3end_transcriptional_regulator,_tetR_family_1263656..1263806_NEGATIVE 320 49 2 125 82 NC_002950:PG2080|3end_adenosylmethionine--8-amino-7-oxononanoate_transaminase_2179378..2179528_NEGATIVE 319 62 21 86 51 NC_002950:PG1995|3end_hypothetical_protein_2086014..2086164_POSITIVE 312 56 19 148 104 NC_002950:PG1209|3end_hypothetical_protein_1289075..1289225_POSITIVE 310 58 12 43 5 NC_002950:PG0212|3end_precorrin-6Y_C5,15-methyltransferase,_decarboxylating_247824..247974_NEGATIVE 308 68 21 147 102 NC_002950:PG0676|3end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_726514..726664_NEGATIVE 305 58 11 106 57 NC_002950:PG1366|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1446076..1446226_NEGATIVE 304 60 12 70 14 NC_002950:PG0286|3end_hypothetical_protein_320454..320604_POSITIVE 299 68 28 144 112 NC_002950:PG1383|3end_amino_acid_exporter,_putative_1463387..1463537_POSITIVE 299 64 28 53 12 NC_002950:PG1234|3end_hypothetical_protein_1310320..1310470_POSITIVE 295 40 1 60 11 NC_002950:PG0602|3end_hypothetical_protein_659620..659770_POSITIVE 293 137 97 150 104 NC_002950:PG2048|3end_hypothetical_protein_2148134..2148284_NEGATIVE 293 66 25 52 18 NC_002950:PG1752|3end_hypothetical_protein_1838698..1838848_POSITIVE 293 67 29 55 21 NC_002950:PG1288|3end_GDP-mannose_4,6-dehydratase_1367128..1367278_POSITIVE 293 66 30 101 61 NC_002950:PG0139|3end_membrane-bound_lytic_murein_transglycosylase_D,_putative_161786..161936_NEGATIVE 291 49 1 132 71 NC_002950:PG1379|3end_ABC_transporter,_periplasmic_substrate-binding_protein,_putative_1459955..1460105_POSITIVE 289 55 11 63 6 NC_002950:PG1306|3end_metallo-beta-lactamase_family_protein_1386543..1386693_NEGATIVE 289 56 13 120 61 NC_002950:PG0619|3end_alkyl_hydroperoxide_reductase,_F_subunit_672731..672881_POSITIVE