Origin IGS: gtgtttttctccttaaattttatattctattttctttttgatactcttcttaggcggcgccgccgtcagagcttgactttatcaatctctttgactaaactttgagcctaaggtctcaaagtttgcgcgaatagcgccactgcgaagagtatcgtctttggctcgcttcgctcactattgcaaagctgaacaattttttatctttcttcatagtttattgtcgtctcggacaagatttttcgagttttctagc .........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 gctagaaaactcgaaaaatcttgtccgagacgacaataaactatgaagaaagataaaaaattgttcagctttgcaatagtgagcgaagcgagccaaagacgatactcttcgcagtggcgctattcgcgcaaactttgagaccttaggctcaaagtttagtcaaagagattgataaagtcaagctctgacggcggcgccgcctaagaagagtatcaaaaagaaaatagaatataaaatttaaggagaaaaacac Mask Tandem Repeat Region ================================================ gtgtttttctccttaaattttatattctattttctttttgatactcttcttaggcggcgccgccgtcagagcttgactttatcaatctctttgactaaactttgagcctaaggtctcaaagtttgcgcgaatagcgccactgcgaagagtatcgtctttggctcgcttcgctcactattgcaaagctgaacaattttttatctttcttcatagtttattgtcgtctcggacaagatttttcgagttttctagc Find is-nt database================================================ Query_seq: SSA_2007:SSA_2008|SSA_2007:SSA_2008:Chaperone protein dnaK/HSP70, putative:Molecular chaperone GrpE (HSP-70 cofactor), putative:<-<-:2009363..2009615 253 gtgtttttctccttaaattttatattctattttctttttgatactcttcttaggcggcgccgccgtcagagcttgactttatcaatctctttgactaaactttgagcctaaggtctcaaagtttgcgcgaatagcgccactgcgaagagtatcgtctttggctcgcttcgctcactattgcaaagctgaacaattttttatctttcttcatagtttattgtcgtctcggacaagatttttcgagttttctagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2007:SSA_2008|SSA_2007:SSA_2008:Chaperone protein dnaK/HSP70, putative:Molecular chaperone GrpE (HSP-70 cofactor), putative:<-<-:2009363..2009615 253 gtgtttttctccttaaattttatattctattttctttttgatactcttcttaggcggcgccgccgtcagagcttgactttatcaatctctttgactaaactttgagcctaaggtctcaaagtttgcgcgaatagcgccactgcgaagagtatcgtctttggctcgcttcgctcactattgcaaagctgaacaattttttatctttcttcatagtttattgtcgtctcggacaagatttttcgagttttctagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2007:SSA_2008|SSA_2007:SSA_2008:Chaperone protein dnaK/HSP70, putative:Molecular chaperone GrpE (HSP-70 cofactor), putative:<-<-:2009363..2009615 253 gtgtttttctccttaaattttatattctattttctttttgatactcttcttaggcggcgccgccgtcagagcttgactttatcaatctctttgactaaactttgagcctaaggtctcaaagtttgcgcgaatagcgccactgcgaagagtatcgtctttggctcgcttcgctcactattgcaaagctgaacaattttttatctttcttcatagtttattgtcgtctcggacaagatttttcgagttttctagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtgtttttctccttaaattttatattctattttctttttgatactcttcttaggcggcgccgccgtcagagcttgactttatcaatctctttgactaaactttgagcctaaggtctcaaagtttgcgcgaatagcgccactgcgaagagtatcgtctttggctcgcttcgctcactattgcaaagctgaacaattttttatctttcttcatagtttattgtcgtctcggacaagatttttcgagttttctagc Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 1 End: 102 M F F S L N F I F Y F L F D T L L R R R R R Q S L T L S I S L T K L ....................................................................................................................................................... Protein_Len: 41 Strand: + Start: 131 End: 253 .................................................................................................................................. M A P L R R V S S L A R F A H Y C K A E Q F F I F L H S L L S S R T R F F E F S S Protein_Len: 31 Strand: - Start: 119 End: 211 ...................................................................................................................... L K R S Y R W Q S S Y R R Q S A E S V I A F S F L K K D K K M .......................................... gtgtttttctccttaaattttatattctattttctttttgatactcttcttaggcggcgccgccgtcagagcttgactttatcaatctctttgactaaactttgagcctaaggtctcaaagtttgcgcgaatagcgccactgcgaagagtatcgtctttggctcgcttcgctcactattgcaaagctgaacaattttttatctttcttcatagtttattgtcgtctcggacaagatttttcgagttttctagc 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: 82 Start: 72 End: 101 .......................................................................CTTGACTTTATCAATCTCTTTGACTAAACT........................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtgtttttctccttaaattttatattctattttctttttgatactcttcttaggcggcgccgccgtcagagcttgactttatcaatctctttgactaaactttgagcctaaggtctcaaagtttgcgcgaatagcgccactgcgaagagtatcgtctttggctcgcttcgctcactattgcaaagctgaacaattttttatctttcttcatagtttattgtcgtctcggacaagatttttcgagttttctagc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 54 HP_score: -4.0 Tail_Score: -3.67588 Start: 69 End: 89 Full_Region: GCGGCGCCGCCGTCA GAGCTTGA CTTTA TCAATCTC TTTGACTAAACTTTG ....................................................................GAGCTTGACTTTATCAATCTC.................................................................................................................................................................... TransTerm Strand: - Conf: 70 HP_score: -8.1 Tail_Score: -3.72695 Start: 100 End: 121 Full_Region: cgctattcgcgcaaa ctttgagacc tta ggctcaaag tttagtcaaagagat ...................................................................................................ctttgagaccttaggctcaaag.................................................................................................................................... Find igs database================================================ Query_seq: SSA_2007:SSA_2008|SSA_2007:SSA_2008:Chaperone protein dnaK/HSP70, putative:Molecular chaperone GrpE (HSP-70 cofactor), putative:<-<-:2009363..2009615 253 gtgtttttctccttaaattttatattctattttctttttgatactcttcttaggcggcgccgccgtcagagcttgactttatcaatctctttgactaaactttgagcctaaggtctcaaagtttgcgcgaatagcgccactgcgaagagtatcgtctttggctcgcttcgctcactattgcaaagctgaacaattttttatctttcttcatagtttattgtcgtctcggacaagatttttcgagttttctagc Intra-Species Hit: Count: 1 Min: 1 Max: 253 Len: 253 Subject: NC_009009_SSA_2007_SSA_2008|Chaperone protein dnaK/HSP70, putative:Molecular chaperone GrpE (HSP-70 cofactor), putative|NEGATIVE:NEGATIVE|[2009363,2009615]|253 HSP 1 e-value: 1.0E-141 bit: 502.0 Len: 253 Query Start:1 Query End:253 Subject Strand: POSITIVE Subject Start: 1 Subject End: 253 gtgtttttctccttaaattttatattctattttctttttgatactcttcttaggcggcgccgccgtcagagcttgactttatcaatctctttgactaaactttgagcctaaggtctcaaagtttgcgcgaatagcgccactgcgaagagtatcgtctttggctcgcttcgctcactattgcaaagctgaacaattttttatctttcttcatagtttattgtcgtctcggacaagatttttcgagttttctagc gtgtttttctccttaaattttatattctattttctttttgatactcttcttaggcggcgccgccgtcagagcttgactttatcaatctctttgactaaactttgagcctaaggtctcaaagtttgcgcgaatagcgccactgcgaagagtatcgtctttggctcgcttcgctcactattgcaaagctgaacaattttttatctttcttcatagtttattgtcgtctcggacaagatttttcgagttttctagc Inter-species Hit: Count: 3 Min: 30 Max: 234 Len: 205 Subject: NC_008533_SPD_0459_SPD_0460|heat shock protein GrpE:chaperone protein DnaK|POSITIVE:POSITIVE|[469109,469587]|479 HSP 1 e-value: 5.0E-72 bit: 272.0 Len: 205 Query Start:30 Query End:234 Subject Strand: NEGATIVE Subject Start: 245 Subject End: 448 .............................ttttctttttgatactcttcttaggcggcgccgccgtcagagcttgactttatcaatctctttgactaaactttgagcctaaggtctcaaagtttgcgcgaatagcgccactgcgaagagtatcgtctttggctcgcttcgctcactattgcaaagctgaacaattttttatctttcttcatagtttattgtcgtctcggacaag................... .............................ttttctttttgatactcttcttaagtggcgacgccgtcagagcttgacttcgtcaatctctttgactaaactttgagcctaaggtctcaaaatttgcgcaaatagcaccacggcgaagagtatcgtctttggttcgcttcgctcactattacaaagccaaac-atattttatctttcttcatagtttattgtcgtttcggacaag................... Subject: NC_003098_spr0454_spr0455|Heat-shock protein (activation of DnaK):molecular chaperone DnaK|POSITIVE:POSITIVE|[461579,462057]|479 HSP 1 e-value: 5.0E-72 bit: 272.0 Len: 205 Query Start:30 Query End:234 Subject Strand: NEGATIVE Subject Start: 245 Subject End: 448 .............................ttttctttttgatactcttcttaggcggcgccgccgtcagagcttgactttatcaatctctttgactaaactttgagcctaaggtctcaaagtttgcgcgaatagcgccactgcgaagagtatcgtctttggctcgcttcgctcactattgcaaagctgaacaattttttatctttcttcatagtttattgtcgtctcggacaag................... .............................ttttctttttgatactcttcttaagtggcgacgccgtcagagcttgacttcgtcaatctctttgactaaactttgagcctaaggtctcaaaatttgcgcaaatagcaccacggcgaagagtatcgtctttggttcgcttcgctcactattacaaagccaaac-atattttatctttcttcatagtttattgtcgtttcggacaag................... Subject: NC_003028_SP_0516_SP_0517|heat shock protein GrpE:molecular chaperone DnaK|POSITIVE:POSITIVE|[496997,497484]|488 HSP 1 e-value: 3.0E-61 bit: 236.0 Len: 179 Query Start:56 Query End:234 Subject Strand: NEGATIVE Subject Start: 245 Subject End: 422 .......................................................ggcgccgccgtcagagcttgactttatcaatctctttgactaaactttgagcctaaggtctcaaagtttgcgcgaatagcgccactgcgaagagtatcgtctttggctcgcttcgctcactattgcaaagctgaacaattttttatctttcttcatagtttattgtcgtctcggacaag................... .......................................................ggcgacgccgtcagagcttgacttcgtcaatctctttgactaaactttgagcctaaggtctcaaaatttgcgcaaatagcgccacggcgaagagtatcgtgtttggttcgcttcgctcactattacaaagccaaac-atattttatctttcttcatagtttattgtcgtttcggacaag................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCUUUUUGAUACUCUUCUUAGGCGGCGCCGCCGUCAGAGCUUGACUUUAUCAAUCUCUUUGACUAAACUUUGAGCCUAAGGUCUCAAAGUUUGCGCGAAUAGCGCCACUGCGAAGAGUAUCGUCUUUGGCUCGCUUCGCUCACUAUUGCAAAGCUGAACAAUUUUUUAUCUUUCUUCAUAGUUUAUUGUCGUCUCGGACAAG ..........((((((((((.(((..((((((((.(((((((.((((.....))))...))))))).((((((((((((...)).))))))))))..)))....))))).))).))))))))))((((..(((..((((.((........)).))))...(((((...((((........))))...))))).)))..))))... (-66.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUGUCCGAGACGACAAUAAACUAUGAAGAAAGAUAAAAAAUUGUUCAGCUUUGCAAUAGUGAGCGAAGCGAGCCAAAGACGAUACUCUUCGCAGUGGCGCUAUUCGCGCAAACUUUGAGACCUUAGGCUCAAAGUUUAGUCAAAGAGAUUGAUAAAGUCAAGCUCUGACGGCGGCGCCGCCUAAGAAGAGUAUCAAAAAGAAAA .(((((......)))))..........................((((.(((((((........))))))))))).......((((((((((...(((((((....(((..((((((((((.((...)))))))))))).((((..(((.(((((...))))).))))))).))))))))))....)))))))))).......... (-70.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1016 60 11 180 131 NC_009009:SSA_2007|5end_Chaperone_protein_dnaK/HSP70,_putative_2009272..2009502_NEGATIVE 464 46 2 228 174 NC_009009:SSA_1998|5end_Trigger_factor,_putative_1996331..1996561_NEGATIVE 361 51 13 175 124 NC_009009:SSA_0377|5end_ABC-type_methionine_transporter,_permease_component,_putative_366446..366676_POSITIVE 355 48 2 57 1 NC_009009:SSA_2002|5end_tRNA_pseudouridine_synthase_A,_putative_1998959..1999189_NEGATIVE 352 156 111 168 113 NC_009009:SSA_0585|5end_hypothetical_protein_576937..577167_POSITIVE 350 137 91 70 16 NC_009009:SSA_1948|5end_Oligopeptide-binding_lipoprotein_precursor,_putative_1942170..1942400_NEGATIVE 349 147 102 142 90 NC_009009:SSA_2228|5end_Acetyltransferase_(GNAT)_family,_putative_2228768..2228998_NEGATIVE 346 69 23 55 8 NC_009009:SSA_0791|5end_UDP-N-acetylglucosamine-like_protein,_putative_773345..773575_POSITIVE 340 146 104 170 125 NC_009009:SSA_0808|5end_hypothetical_protein_790771..791001_POSITIVE 333 60 15 152 109 NC_009009:SSA_0334|5end_Diphosphomevalonate_decarboxylase,_putative_327855..328085_POSITIVE 329 120 76 205 150 NC_009009:SSA_1952|5end_ABC-type_Fe-S_cluster_assembly_transporter,_permease_component,_putative_1949624..1949854_NEGATIVE 329 60 15 59 2 NC_009009:SSA_1466|5end_Prephenate_dehydrogenase,_putative_1473111..1473341_NEGATIVE 326 140 91 75 8 NC_009009:SSA_1190|5end_Conserved_uncharacterized_protein_1218137..1218367_NEGATIVE 324 145 105 227 182 NC_009009:SSA_2239|5end_Conserved_uncharacterized_cytosolic_protein_2237233..2237463_NEGATIVE 322 66 27 229 188 NC_009009:SSA_2071|5end_hypothetical_protein_2074766..2074996_NEGATIVE 322 150 101 84 34 NC_009009:SSA_0491|5end_Alpha-ribazole-5'-phosphate_phosphatase,_putative_490961..491191_POSITIVE 320 148 107 74 30 NC_009009:SSA_1775|5end_Potassium_uptake_protein,_Trk_family,_putative_1761284..1761514_POSITIVE 319 64 24 59 7 NC_009009:SSA_2270|5end_Aspartyl-tRNA_synthetase,_putative_2272068..2272298_NEGATIVE 319 58 15 151 100 NC_009009:SSA_1804|5end_NADPH-flavin_oxidoreductase,_putative_1788668..1788898_NEGATIVE 317 65 24 54 5 NC_009009:SSA_2361|5end_L-serine_dehydratase_beta_subunit_2364028..2364258_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 464 46 2 148 94 NC_009009:SSA_1999|3end_hypothetical_protein_1996411..1996561_NEGATIVE 361 50 4 131 85 NC_009009:SSA_2260|3end_DNA_mismatch_repair_protein_hexA,_putative_2255601..2255751_NEGATIVE 357 108 61 86 27 NC_009009:SSA_2119|3end_Pentose-5-phosphate-3-epimerase,_putative_2120439..2120589_NEGATIVE 349 147 102 89 37 NC_009009:SSA_2229|3end_hypothetical_protein_2228821..2228971_NEGATIVE 324 159 112 108 27 NC_009009:SSA_0686|3end_Fe2+/Zn2+_uptake_regulation_protein,_putative_670079..670229_POSITIVE 322 150 101 87 37 NC_009009:SSA_0490|3end_Cobalamin_5'-phosphate_synthase,_putative_491044..491194_POSITIVE 318 147 106 88 35 NC_009009:SSA_2227|3end_Acetyl_transferase,_putative_2227716..2227866_NEGATIVE 316 60 17 55 8 NC_009009:SSA_1822|3end_hypothetical_protein_1810871..1811021_NEGATIVE 312 64 30 68 20 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE 312 55 15 151 109 NC_009009:SSA_0263|3end_Zinc_metalloproteinase_in_scaA_5'region,_putative_258246..258396_POSITIVE 312 46 4 136 87 NC_009009:SSA_0259|3end_Thiol_peroxidase,_putative_253013..253163_NEGATIVE 307 50 5 129 87 NC_009009:SSA_2242|3end_hypothetical_protein_2238121..2238271_NEGATIVE 306 52 13 133 96 NC_009009:SSA_1957|3end_Glycosyl_transferase_N-acetylglucosaminyltransferase,_putative_1953504..1953654_NEGATIVE 305 127 81 144 96 NC_009009:SSA_0326|3end_Conserved_uncharacterized_BCR,_YbaB_family_319524..319674_NEGATIVE 304 140 92 56 9 NC_009009:SSA_2318|3end_PilB-like_pili_biogenesis_ATPase,_putative_2319412..2319562_NEGATIVE 304 43 2 67 17 NC_009009:SSA_1805|3end_Primosomal_protein_DnaI,_putative_1788665..1788815_NEGATIVE 304 157 111 79 24 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 303 48 9 55 24 NC_009009:SSA_1443|3end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1445944..1446094_NEGATIVE 303 145 104 117 56 NC_009009:SSA_1267|3end_crcB-like_protein_2,_putative_1290973..1291123_NEGATIVE 303 120 72 68 3 NC_009009:SSA_0315|3end_Transcriptional_regulator,_MarR_family,_putative_310646..310796_POSITIVE