Origin IGS: ttttggttaataaagcctgatacacttgcctctggcgagtatgtcaggtttttctttttgctttcagttcttgagctcaataaaagatttaggtgcttcgagaaagttgattgatgaactttcttggagtttttattttgcagtaaagtgaagaaatttgtctctaaacaaaagaaaatgataagagacaaacatttttaaagacttaaaataaaaagtttaaaattttagtaaaagtacttttaaatcataggtgtttatgataaaatgaagggaacatttctttttgtgtaatgattgcgagatcattgaaaaagtttaggaggtaagaa .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttcttacctcctaaactttttcaatgatctcgcaatcattacacaaaaagaaatgttcccttcattttatcataaacacctatgatttaaaagtacttttactaaaattttaaactttttattttaagtctttaaaaatgtttgtctcttatcattttcttttgtttagagacaaatttcttcactttactgcaaaataaaaactccaagaaagttcatcaatcaactttctcgaagcacctaaatcttttattgagctcaagaactgaaagcaaaaagaaaaacctgacatactcgccagaggcaagtgtatcaggctttattaaccaaaa Mask Tandem Repeat Region ================================================ ttttggttaataaagcctgatacacttgcctctggcgagtatgtcaggtttttctttttgctttcagttcttgagctcaataaaagatttaggtgcttcgagaaagttgattgatgaactttcttggagtttttattttgcagtaaagtgaagaaatttgtctctaaacaaaagaaaatgataagagacaaacatttttaaagacttaaaataaaaagtttaaaattttagtaaaagtacttttaaatcataggtgtttatgataaaatgaagggaacatttctttttgtgtaatgattgcgagatcattgaaaaagtttaggaggtaagaa Find is-nt database================================================ Query_seq: SSA_0683:SSA_0684|SSA_0683:SSA_0684:DNA-binding protein HU, putative:Fibril-like structure subunit FibA, putative:->->:664800..665131 332 ttttggttaataaagcctgatacacttgcctctggcgagtatgtcaggtttttctttttgctttcagttcttgagctcaataaaagatttaggtgcttcgagaaagttgattgatgaactttcttggagtttttattttgcagtaaagtgaagaaatttgtctctaaacaaaagaaaatgataagagacaaacatttttaaagacttaaaataaaaagtttaaaattttagtaaaagtacttttaaatcataggtgtttatgataaaatgaagggaacatttctttttgtgtaatgattgcgagatcattgaaaaagtttaggaggtaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0683:SSA_0684|SSA_0683:SSA_0684:DNA-binding protein HU, putative:Fibril-like structure subunit FibA, putative:->->:664800..665131 332 ttttggttaataaagcctgatacacttgcctctggcgagtatgtcaggtttttctttttgctttcagttcttgagctcaataaaagatttaggtgcttcgagaaagttgattgatgaactttcttggagtttttattttgcagtaaagtgaagaaatttgtctctaaacaaaagaaaatgataagagacaaacatttttaaagacttaaaataaaaagtttaaaattttagtaaaagtacttttaaatcataggtgtttatgataaaatgaagggaacatttctttttgtgtaatgattgcgagatcattgaaaaagtttaggaggtaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0683:SSA_0684|SSA_0683:SSA_0684:DNA-binding protein HU, putative:Fibril-like structure subunit FibA, putative:->->:664800..665131 332 ttttggttaataaagcctgatacacttgcctctggcgagtatgtcaggtttttctttttgctttcagttcttgagctcaataaaagatttaggtgcttcgagaaagttgattgatgaactttcttggagtttttattttgcagtaaagtgaagaaatttgtctctaaacaaaagaaaatgataagagacaaacatttttaaagacttaaaataaaaagtttaaaattttagtaaaagtacttttaaatcataggtgtttatgataaaatgaagggaacatttctttttgtgtaatgattgcgagatcattgaaaaagtttaggaggtaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttggttaataaagcctgatacacttgcctctggcgagtatgtcaggtttttctttttgctttcagttcttgagctcaataaaagatttaggtgcttcgagaaagttgattgatgaactttcttggagtttttattttgcagtaaagtgaagaaatttgtctctaaacaaaagaaaatgataagagacaaacatttttaaagacttaaaataaaaagtttaaaattttagtaaaagtacttttaaatcataggtgtttatgataaaatgaagggaacatttctttttgtgtaatgattgcgagatcattgaaaaagtttaggaggtaagaa Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 10 End: 111 ......... M K P D T L A S G E Y V R F F F L L S V L E L N K R F R C F E K V D ............................................................................................................................................................................................................................. Protein_Len: 44 Strand: + Start: 17 End: 148 ................ M I H L P L A S M S G F S F C F Q F L S S I K D L G A S R K L I D E L S W S F Y F A V K ........................................................................................................................................................................................ Protein_Len: 60 Strand: - Start: 3 End: 191 .. F G S V S A E P S Y T L N K K K S E T R S S L L L N L H K S F T S Q H V K K S N K N Q L L T F F N T E L C F F I I L S M ............................................................................................................................................. ttttggttaataaagcctgatacacttgcctctggcgagtatgtcaggtttttctttttgctttcagttcttgagctcaataaaagatttaggtgcttcgagaaagttgattgatgaactttcttggagtttttattttgcagtaaagtgaagaaatttgtctctaaacaaaagaaaatgataagagacaaacatttttaaagacttaaaataaaaagtttaaaattttagtaaaagtacttttaaatcataggtgtttatgataaaatgaagggaacatttctttttgtgtaatgattgcgagatcattgaaaaagtttaggaggtaagaa 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: 240 End: 269 ...............................................................................................................................................................................................................................................CTTTTAAATCATAGGTGTTTATGATAAAAT............................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttggttaataaagcctgatacacttgcctctggcgagtatgtcaggtttttctttttgctttcagttcttgagctcaataaaagatttaggtgcttcgagaaagttgattgatgaactttcttggagtttttattttgcagtaaagtgaagaaatttgtctctaaacaaaagaaaatgataagagacaaacatttttaaagacttaaaataaaaagtttaaaattttagtaaaagtacttttaaatcataggtgtttatgataaaatgaagggaacatttctttttgtgtaatgattgcgagatcattgaaaaagtttaggaggtaagaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 95 HP_score: -8.3 Tail_Score: -5.46706 Start: 96 End: 129 Full_Region: TAAAAGATTTAGGTG CTTCGAGAAAGTTGA TTGA TGAACTTTCTTGGAG TTTTTATTTTGCAGT ...............................................................................................CTTCGAGAAAGTTGATTGATGAACTTTCTTGGAG........................................................................................................................................................................................................... TransTerm Strand: + Conf: 44 HP_score: -3.4 Tail_Score: -2.60776 Start: 157 End: 192 Full_Region: AGTAAAGTGAAGAAA TTTGTCTCTAAACA AAAGAAAA TGATAAGAGACAAA CATTTTTAAAGACTT ............................................................................................................................................................TTTGTCTCTAAACAAAAGAAAATGATAAGAGACAAA............................................................................................................................................ TransTerm Strand: - Conf: 59 HP_score: -3.4 Tail_Score: -4.29929 Start: 157 End: 192 Full_Region: aagtctttaaaaatg tttgtctcttatca ttttcttt tgtttagagacaaa tttcttcactttact ............................................................................................................................................................tttgtctcttatcattttcttttgtttagagacaaa............................................................................................................................................ Find igs database================================================ Query_seq: SSA_0683:SSA_0684|SSA_0683:SSA_0684:DNA-binding protein HU, putative:Fibril-like structure subunit FibA, putative:->->:664800..665131 332 ttttggttaataaagcctgatacacttgcctctggcgagtatgtcaggtttttctttttgctttcagttcttgagctcaataaaagatttaggtgcttcgagaaagttgattgatgaactttcttggagtttttattttgcagtaaagtgaagaaatttgtctctaaacaaaagaaaatgataagagacaaacatttttaaagacttaaaataaaaagtttaaaattttagtaaaagtacttttaaatcataggtgtttatgataaaatgaagggaacatttctttttgtgtaatgattgcgagatcattgaaaaagtttaggaggtaagaa Intra-Species Hit: Count: 1 Min: 1 Max: 332 Len: 332 Subject: NC_009009_SSA_0683_SSA_0684|DNA-binding protein HU, putative:Fibril-like structure subunit FibA, putative|POSITIVE:POSITIVE|[664800,665131]|332 HSP 1 e-value: 6.0E-88 bit: 325.0 Len: 164 Query Start:1 Query End:164 Subject Strand: POSITIVE Subject Start: 1 Subject End: 164 ttttggttaataaagcctgatacacttgcctctggcgagtatgtcaggtttttctttttgctttcagttcttgagctcaataaaagatttaggtgcttcgagaaagttgattgatgaactttcttggagtttttattttgcagtaaagtgaagaaatttgtctc........................................................................................................................................................................ ttttggttaataaagcctgatacacttgcctctggcgagtatgtcaggtttttctttttgctttcagttcttgagctcaataaaagatttaggtgcttcgagaaagttgattgatgaactttcttggagtttttattttgcagtaaagtgaagaaatttgtctc........................................................................................................................................................................ HSP 2 e-value: 8.0E-41 bit: 168.0 Len: 85 Query Start:248 Query End:332 Subject Strand: POSITIVE Subject Start: 248 Subject End: 332 .......................................................................................................................................................................................................................................................tcataggtgtttatgataaaatgaagggaacatttctttttgtgtaatgattgcgagatcattgaaaaagtttaggaggtaagaa .......................................................................................................................................................................................................................................................tcataggtgtttatgataaaatgaagggaacatttctttttgtgtaatgattgcgagatcattgaaaaagtttaggaggtaagaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUGGUUAAUAAAGCCUGAUACACUUGCCUCUGGCGAGUAUGUCAGGUUUUUCUUUUUGCUUUCAGUUCUUGAGCUCAAUAAAAGAUUUAGGUGCUUCGAGAAAGUUGAUUGAUGAACUUUCUUGGAGUUUUUAUUUUGCAGUAAAGUGAAGAAAUUUGUCUCUAAACAAAAGAAAAUGAUAAGAGACAAACAUUUUUAAAGACUUAAAAUAAAAAGUUUAAAAUUUUAGUAAAAGUACUUUUAAAUCAUAGGUGUUUAUGAUAAAAUGAAGGGAACAUUUCUUUUUGUGUAAUGAUUGCGAGAUCAUUGAAAAAGUUUAGGAGGUAAGAA ...........(((((((((((.(((((((...))))))).)))))))))))...((((((((((.((((((....(((.((((((((((....((((((((((((((........))))))))))))))((((((((((.(((....((((((..(((((((((...((........))...)))))))))..))))))...)))))))))))))..................)))).)))))).(((((((....)))))))....))).))))))....((((((...((((((((....))))))))))))))....)))))))))). (-91.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUUACCUCCUAAACUUUUUCAAUGAUCUCGCAAUCAUUACACAAAAAGAAAUGUUCCCUUCAUUUUAUCAUAAACACCUAUGAUUUAAAAGUACUUUUACUAAAAUUUUAAACUUUUUAUUUUAAGUCUUUAAAAAUGUUUGUCUCUUAUCAUUUUCUUUUGUUUAGAGACAAAUUUCUUCACUUUACUGCAAAAUAAAAACUCCAAGAAAGUUCAUCAAUCAACUUUCUCGAAGCACCUAAAUCUUUUAUUGAGCUCAAGAACUGAAAGCAAAAAGAAAAACCUGACAUACUCGCCAGAGGCAAGUGUAUCAGGCUUUAUUAACCAAAA (((((..(((............((((((......)))))).....((((((........((((.....((((((......)))))).....((((....))))............((((((((((.(((..........((((((((((...((........))...))))))))))...........)))..)))))))))).....((((((((........)))))))).))))........))))))...)))...)))))...............(((.(((((.(((((.(((...))).))))).))))).)))........... (-57.59) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 326 60 16 70 23 NC_009009:SSA_1874|5end_YorfE_protein,_putative_1870295..1870525_POSITIVE 312 79 32 215 160 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 301 138 100 167 116 NC_009009:SSA_1117|5end_hypothetical_protein_1142743..1142973_POSITIVE 299 68 23 159 105 NC_009009:SSA_1659|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1656819..1657049_NEGATIVE 298 76 31 186 143 NC_009009:SSA_2123|5end_Dimethyladenosine_transferase,_putative_2128536..2128766_NEGATIVE 295 78 32 78 28 NC_009009:SSA_2102|5end_Conserved_uncharacterized_protein_2106410..2106640_NEGATIVE 291 69 21 226 171 NC_009009:SSA_1735|5end_UreX,_putative_1721072..1721302_NEGATIVE 289 79 33 209 161 NC_009009:SSA_0216|5end_Histidine_kinase,_putative_211877..212107_POSITIVE 288 80 31 63 24 NC_009009:SSA_0834|5end_Accessory_secretory_protein_Asp2,_putative_819510..819740_POSITIVE 288 49 11 121 73 NC_009009:SSA_0608|5end_Macrolide-efflux_protein,_putative_598184..598414_NEGATIVE 288 55 16 42 1 NC_009009:SSA_0219|5end_PTS_system,_sugar-specific_enzyme_IIA_component,_putative_215367..215597_POSITIVE 281 70 21 137 93 NC_009009:SSA_0163|5end_hypothetical_protein_162127..162357_POSITIVE 280 77 31 121 77 NC_009009:SSA_2071|5end_hypothetical_protein_2074766..2074996_NEGATIVE 280 54 11 103 53 NC_009009:SSA_1773|5end_hypothetical_protein_1760092..1760322_NEGATIVE 280 80 31 185 122 NC_009009:SSA_0485|5end_Porphobilinogen_deaminase,_putative_485732..485962_POSITIVE 279 78 31 166 121 NC_009009:SSA_2231|5end_Heme/copper-type_cytochrome/quinol_oxidases,_subunit_1,_putative_2232928..2233158_NEGATIVE 279 57 14 85 44 NC_009009:SSA_1897|5end_Ribosomal_protein_HS6-type_(S12/L30/L7a),_putative_1894450..1894680_NEGATIVE 277 127 84 228 191 NC_009009:SSA_0783|5end_Proton-translocating_ATPase,_F0_sector,_subunit_a,_putative_766815..767045_POSITIVE 275 56 12 194 140 NC_009009:SSA_0508|5end_Conserved_uncharacterized_protein,_possible_phosphoserine_phosphatase_506668..506898_POSITIVE 274 80 34 183 144 NC_009009:SSA_0031|5end_Glutamine_phosphoribosylpyrophosphate_amidotransferase,_putative_36439..36669_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 451 52 12 79 39 NC_009009:SSA_0683|3end_DNA-binding_protein_HU,_putative_664739..664889_POSITIVE 346 77 31 144 95 NC_009009:SSA_0753|3end_Foldase_protein_prsA_precursor,_putative_736055..736205_POSITIVE 313 68 21 132 92 NC_009009:SSA_1686|3end_hypothetical_protein_1680470..1680620_POSITIVE 301 138 100 96 45 NC_009009:SSA_1116|3end_hypothetical_protein_1142752..1142902_POSITIVE 291 75 31 116 63 NC_009009:SSA_1127|3end_H2O-forming_NADH_dehydrogenase,_putative_1153187..1153337_POSITIVE 288 80 31 73 34 NC_009009:SSA_0833|3end_Accessory_secretory_protein_Asp1,_putative_819600..819750_POSITIVE 288 49 11 58 10 NC_009009:SSA_0609|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_598247..598397_NEGATIVE 281 70 21 69 25 NC_009009:SSA_0162|3end_hypothetical_protein_162139..162289_POSITIVE 280 77 31 87 43 NC_009009:SSA_2072|3end_Phosphatidate_cytidylyltransferase,_putative_2074800..2074950_NEGATIVE 279 78 31 127 82 NC_009009:SSA_2233|3end_hypothetical_protein_2232967..2233117_NEGATIVE 279 57 14 92 51 NC_009009:SSA_1899|3end_hypothetical_protein_1894443..1894593_NEGATIVE 277 126 91 130 100 NC_009009:SSA_0395|3end_6-phospho-beta-glucosidase,_putative_392580..392730_POSITIVE 274 80 34 88 49 NC_009009:SSA_0030|3end_Phosphoribosylformylglycinamidine_synthase,_putative_36424..36574_POSITIVE 273 110 61 144 85 NC_009009:SSA_1344|3end_Xanthine/uracil_permeases,_putative_1362069..1362219_NEGATIVE 272 78 42 111 68 NC_009009:SSA_2260|3end_DNA_mismatch_repair_protein_hexA,_putative_2255601..2255751_NEGATIVE 272 65 22 151 102 NC_009009:SSA_0616|3end_YlbN-like_protein,_putative_609855..610005_POSITIVE 272 76 31 120 75 NC_009009:SSA_0492|3end_NADH-dependent_flavin_oxidoreductase,_putative_492771..492921_POSITIVE 270 67 28 78 43 NC_009009:SSA_1368|3end_hypothetical_protein_1383748..1383898_NEGATIVE 270 58 14 88 33 NC_009009:SSA_1015|3end_4-hydroxybenzoate_octaprenyltransferase,_putative_1019682..1019832_POSITIVE 270 66 23 151 103 NC_009009:SSA_0263|3end_Zinc_metalloproteinase_in_scaA_5'region,_putative_258246..258396_POSITIVE