Origin IGS: agccttctccaatctagtcagtcttgctttgggaagatgttgattgcgcacccatacttctagcaaaaactcttatttacttttgcgttattatatcaatcaaagtgtactgctgcaattctttatagcacttttagataatccttttttattgataagaatatagtttgaagctatagctaatttttctaatcaaggctattcaagcattgaaaattttgatatgatagtacaaagcaatccagaaacgaggaaaactgatgagtaaaacaaaaaaacttcttgcagccttgggcatccttttctttaacatttttggccttatcgccttcatcgtcttgctcatcagaagcaagaaacgaaaataagaatctgtctgtataattgtctcgtccgattaagaaggacttggcttttttttatttgcttttaaaatagttaccataaaatataaaagaggtttactattt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaatagtaaacctcttttatattttatggtaactattttaaaagcaaataaaaaaaagccaagtccttcttaatcggacgagacaattatacagacagattcttattttcgtttcttgcttctgatgagcaagacgatgaaggcgataaggccaaaaatgttaaagaaaaggatgcccaaggctgcaagaagtttttttgttttactcatcagttttcctcgtttctggattgctttgtactatcatatcaaaattttcaatgcttgaatagccttgattagaaaaattagctatagcttcaaactatattcttatcaataaaaaaggattatctaaaagtgctataaagaattgcagcagtacactttgattgatataataacgcaaaagtaaataagagtttttgctagaagtatgggtgcgcaatcaacatcttcccaaagcaagactgactagattggagaaggct Mask Tandem Repeat Region ================================================ agccttctccaatctagtcagtcttgctttgggaagatgttgattgcgcacccatacttctagcaaaaactcttatttacttttgcgttattatatcaatcaaagtgtactgctgcaattctttatagcacttttagataatccttttttattgataagaatatagtttgaagctatagctaatttttctaatcaaggctattcaagcattgaaaattttgatatgatagtacaaagcaatccagaaacgaggaaaactgatgagtaaaacaaaaaaacttcttgcagccttgggcatccttttctttaacatttttggccttatcgccttcatcgtcttgctcatcagaagcaagaaacgaaaataagaatctgtctgtataattgtctcgtccgattaagaaggacttggcttttttttatttgcttttaaaatagttaccataaaatataaaagaggtttactattt Find is-nt database================================================ Query_seq: SSA_1535:SSA_1536|SSA_1535:SSA_1536:hypothetical protein:Biotin synthase, putative:<-->:1543279..1543748 470 agccttctccaatctagtcagtcttgctttgggaagatgttgattgcgcacccatacttctagcaaaaactcttatttacttttgcgttattatatcaatcaaagtgtactgctgcaattctttatagcacttttagataatccttttttattgataagaatatagtttgaagctatagctaatttttctaatcaaggctattcaagcattgaaaattttgatatgatagtacaaagcaatccagaaacgaggaaaactgatgagtaaaacaaaaaaacttcttgcagccttgggcatccttttctttaacatttttggccttatcgccttcatcgtcttgctcatcagaagcaagaaacgaaaataagaatctgtctgtataattgtctcgtccgattaagaaggacttggcttttttttatttgcttttaaaatagttaccataaaatataaaagaggtttactattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1535:SSA_1536|SSA_1535:SSA_1536:hypothetical protein:Biotin synthase, putative:<-->:1543279..1543748 470 agccttctccaatctagtcagtcttgctttgggaagatgttgattgcgcacccatacttctagcaaaaactcttatttacttttgcgttattatatcaatcaaagtgtactgctgcaattctttatagcacttttagataatccttttttattgataagaatatagtttgaagctatagctaatttttctaatcaaggctattcaagcattgaaaattttgatatgatagtacaaagcaatccagaaacgaggaaaactgatgagtaaaacaaaaaaacttcttgcagccttgggcatccttttctttaacatttttggccttatcgccttcatcgtcttgctcatcagaagcaagaaacgaaaataagaatctgtctgtataattgtctcgtccgattaagaaggacttggcttttttttatttgcttttaaaatagttaccataaaatataaaagaggtttactattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1535:SSA_1536|SSA_1535:SSA_1536:hypothetical protein:Biotin synthase, putative:<-->:1543279..1543748 470 agccttctccaatctagtcagtcttgctttgggaagatgttgattgcgcacccatacttctagcaaaaactcttatttacttttgcgttattatatcaatcaaagtgtactgctgcaattctttatagcacttttagataatccttttttattgataagaatatagtttgaagctatagctaatttttctaatcaaggctattcaagcattgaaaattttgatatgatagtacaaagcaatccagaaacgaggaaaactgatgagtaaaacaaaaaaacttcttgcagccttgggcatccttttctttaacatttttggccttatcgccttcatcgtcttgctcatcagaagcaagaaacgaaaataagaatctgtctgtataattgtctcgtccgattaagaaggacttggcttttttttatttgcttttaaaatagttaccataaaatataaaagaggtttactattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agccttctccaatctagtcagtcttgctttgggaagatgttgattgcgcacccatacttctagcaaaaactcttatttacttttgcgttattatatcaatcaaagtgtactgctgcaattctttatagcacttttagataatccttttttattgataagaatatagtttgaagctatagctaatttttctaatcaaggctattcaagcattgaaaattttgatatgatagtacaaagcaatccagaaacgaggaaaactgatgagtaaaacaaaaaaacttcttgcagccttgggcatccttttctttaacatttttggccttatcgccttcatcgtcttgctcatcagaagcaagaaacgaaaataagaatctgtctgtataattgtctcgtccgattaagaaggacttggcttttttttatttgcttttaaaatagttaccataaaatataaaagaggtttactattt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 24 End: 125 ....................... M L W E D V D C A P I L L A K T L I Y F C V I I S I K V Y C C N S L ......................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 40 Strand: + Start: 44 End: 163 ........................................... M R T H T S S K N S Y L L L R Y Y I N Q S V L L Q F F I A L L D N P F L L I R I ................................................................................................................................................................................................................................................................................................................... Protein_Len: 30 Strand: + Start: 176 End: 265 ............................................................................................................................................................................... M A N F S N Q G Y S S I E N F D M I V Q S N P E T R K T D E ............................................................................................................................................................................................................. Protein_Len: 42 Strand: + Start: 240 End: 365 ............................................................................................................................................................................................................................................... M Q K R G K L M S K T K K L L A A L G I L F F N I F G L I A F I V L L I R S K K R K ......................................................................................................... Protein_Len: 33 Strand: + Start: 283 End: 381 .......................................................................................................................................................................................................................................................................................... M Q P W A S F S L T F L A L S P S S S C S S E A R N E N K N L S V ......................................................................................... Protein_Len: 60 Strand: - Start: 206 End: 385 ............................................................................................................................................................................................................. A N F I K I H Y Y L A I W F R P F S I L L V F F S R A A K P M R K K L M K P R I A K M T K S M L L L F R F Y S D T Q I M ..................................................................................... Protein_Len: 60 Strand: - Start: 192 End: 398 ............................................................................................................................................................................................... Q Y S L V F C D L F S S F Q H T F C F F K K C G Q A D K E K V N K A K D G E D D Q E D S A L F S F L F R D T Y N D R G M ........................................................................ agccttctccaatctagtcagtcttgctttgggaagatgttgattgcgcacccatacttctagcaaaaactcttatttacttttgcgttattatatcaatcaaagtgtactgctgcaattctttatagcacttttagataatccttttttattgataagaatatagtttgaagctatagctaatttttctaatcaaggctattcaagcattgaaaattttgatatgatagtacaaagcaatccagaaacgaggaaaactgatgagtaaaacaaaaaaacttcttgcagccttgggcatccttttctttaacatttttggccttatcgccttcatcgtcttgctcatcagaagcaagaaacgaaaataagaatctgtctgtataattgtctcgtccgattaagaaggacttggcttttttttatttgcttttaaaatagttaccataaaatataaaagaggtttactattt 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: 84 Start: 90 End: 119 .........................................................................................ATTGCAGCAGTACACTTTGATTGATATAAT............................................................................................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agccttctccaatctagtcagtcttgctttgggaagatgttgattgcgcacccatacttctagcaaaaactcttatttacttttgcgttattatatcaatcaaagtgtactgctgcaattctttatagcacttttagataatccttttttattgataagaatatagtttgaagctatagctaatttttctaatcaaggctattcaagcattgaaaattttgatatgatagtacaaagcaatccagaaacgaggaaaactgatgagtaaaacaaaaaaacttcttgcagccttgggcatccttttctttaacatttttggccttatcgccttcatcgtcttgctcatcagaagcaagaaacgaaaataagaatctgtctgtataattgtctcgtccgattaagaaggacttggcttttttttatttgcttttaaaatagttaccataaaatataaaagaggtttactattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1535:SSA_1536|SSA_1535:SSA_1536:hypothetical protein:Biotin synthase, putative:<-->:1543279..1543748 470 agccttctccaatctagtcagtcttgctttgggaagatgttgattgcgcacccatacttctagcaaaaactcttatttacttttgcgttattatatcaatcaaagtgtactgctgcaattctttatagcacttttagataatccttttttattgataagaatatagtttgaagctatagctaatttttctaatcaaggctattcaagcattgaaaattttgatatgatagtacaaagcaatccagaaacgaggaaaactgatgagtaaaacaaaaaaacttcttgcagccttgggcatccttttctttaacatttttggccttatcgccttcatcgtcttgctcatcagaagcaagaaacgaaaataagaatctgtctgtataattgtctcgtccgattaagaaggacttggcttttttttatttgcttttaaaatagttaccataaaatataaaagaggtttactattt Intra-Species Hit: Count: 1 Min: 1 Max: 470 Len: 470 Subject: NC_009009_SSA_1535_SSA_1536|hypothetical protein:Biotin synthase, putative|NEGATIVE:POSITIVE|[1543279,1543748]|470 HSP 1 e-value: 0.0 bit: 842.0 Len: 470 Query Start:1 Query End:470 Subject Strand: POSITIVE Subject Start: 1 Subject End: 470 agccttctccaatctagtcagtcttgctttgggaagatgttgattgcgcacccatacttctagcaaaaactcttatttacttttgcgttattatatcaatcaaagtgtactgctgcaattctttatagcacttttagataatccttttttattgataagaatatagtttgaagctatagctaatttttctaatcaaggctattcaagcattgaaaattttgatatgatagtacaaagcaatccagaaacgaggaaaactgatgagtaaaacnnnnnnncttcttgcagccttgggcatccttttctttaacatttttggccttatcgccttcatcgtcttgctcatcagaagcaagaaacgaaaataagaatctgtctgtataattgtctcgtccgattaagaaggacttggcnnnnnnnnatttgcttttaaaatagttaccataaaatataaaagaggtttactattt agccttctccaatctagtcagtcttgctttgggaagatgttgattgcgcacccatacttctagcaaaaactcttatttacttttgcgttattatatcaatcaaagtgtactgctgcaattctttatagcacttttagataatccttttttattgataagaatatagtttgaagctatagctaatttttctaatcaaggctattcaagcattgaaaattttgatatgatagtacaaagcaatccagaaacgaggaaaactgatgagtaaaacaaaaaaacttcttgcagccttgggcatccttttctttaacatttttggccttatcgccttcatcgtcttgctcatcagaagcaagaaacgaaaataagaatctgtctgtataattgtctcgtccgattaagaaggacttggcttttttttatttgcttttaaaatagttaccataaaatataaaagaggtttactattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCCUUCUCCAAUCUAGUCAGUCUUGCUUUGGGAAGAUGUUGAUUGCGCACCCAUACUUCUAGCAAAAACUCUUAUUUACUUUUGCGUUAUUAUAUCAAUCAAAGUGUACUGCUGCAAUUCUUUAUAGCACUUUUAGAUAAUCCUUUUUUAUUGAUAAGAAUAUAGUUUGAAGCUAUAGCUAAUUUUUCUAAUCAAGGCUAUUCAAGCAUUGAAAAUUUUGAUAUGAUAGUACAAAGCAAUCCAGAAACGAGGAAAACUGAUGAGUAAAACAAAAAAACUUCUUGCAGCCUUGGGCAUCCUUUUCUUUAACAUUUUUGGCCUUAUCGCCUUCAUCGUCUUGCUCAUCAGAAGCAAGAAACGAAAAUAAGAAUCUGUCUGUAUAAUUGUCUCGUCCGAUUAAGAAGGACUUGGCUUUUUUUUAUUUGCUUUUAAAAUAGUUACCAUAAAAUAUAAAAGAGGUUUACUAUUU ((((...(((....(((.(((..(((((...((((((((.((......))..))).))))))))))....((((((((...((((..(((((((((((((((((.((((..((((.((....)).)))).(((...(((((.......)))))...)))..)))).))))).(((((((((...............))))))...)))..........))))))))))))..))))((..(((........)))...(((((((((((.((................(((...))).....................(((......)))......)).)))))))))))..)).........))))))))..))).)))..((((((.......))))))....)))...))))..................(((((((.(((...............)))..))))))) (-96.62) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAGUAAACCUCUUUUAUAUUUUAUGGUAACUAUUUUAAAAGCAAAUAAAAAAAAGCCAAGUCCUUCUUAAUCGGACGAGACAAUUAUACAGACAGAUUCUUAUUUUCGUUUCUUGCUUCUGAUGAGCAAGACGAUGAAGGCGAUAAGGCCAAAAAUGUUAAAGAAAAGGAUGCCCAAGGCUGCAAGAAGUUUUUUUGUUUUACUCAUCAGUUUUCCUCGUUUCUGGAUUGCUUUGUACUAUCAUAUCAAAAUUUUCAAUGCUUGAAUAGCCUUGAUUAGAAAAAUUAGCUAUAGCUUCAAACUAUAUUCUUAUCAAUAAAAAAGGAUUAUCUAAAAGUGCUAUAAAGAAUUGCAGCAGUACACUUUGAUUGAUAUAAUAACGCAAAAGUAAAUAAGAGUUUUUGCUAGAAGUAUGGGUGCGCAAUCAACAUCUUCCCAAAGCAAGACUGACUAGAUUGGAGAAGGCU (((((((..(((...............))).)))))))..................((((..((((.........))))....(((((...(((..(((((((((((((((((((((((((.....)))))))).))))).(((......)))....(((((((...((((..(((.....(((((((..((((((((((...(((.....(((..(((........)))..)))..))).................((((.(((.....))).)))).))))))))))...((((((..........((((((..........))))))...........)))))).....))))))).)))..))))..)))))))..............))))))))))))(((((.((((.(((..((......)).)))))))....)))))..)))....))))).....)))) (-95.66) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 955 50 1 141 92 NC_009009:SSA_1535|5end_hypothetical_protein_1543188..1543418_NEGATIVE 385 148 101 59 17 NC_009009:SSA_0522|5end_Ethanolamine_utilization_protein,_putative_521067..521297_POSITIVE 358 49 1 152 104 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 355 330 281 68 12 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 342 355 313 227 181 NC_009009:SSA_0792|5end_hypothetical_protein_774618..774848_POSITIVE 327 330 283 59 7 NC_009009:SSA_0746|5end_Glucosamine-6-phosphate_deaminase,_putative_727078..727308_POSITIVE 326 59 11 200 147 NC_009009:SSA_1345|5end_Bifunctional_pyrimidine_operon_transcriptional_attenuation_protein/uracil_phosphoribosyltransferase,_putative_1363879..1364109_NEGATIVE 320 60 13 221 171 NC_009009:SSA_0242|5end_hypothetical_protein_234978..235208_POSITIVE 318 53 17 37 2 NC_009009:SSA_1262|5end_tRNA_modification_GTPase,_possibly_iron-binding,_putative_1287782..1288012_POSITIVE 313 144 102 208 158 NC_009009:SSA_0929|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_938438..938668_POSITIVE 308 43 1 173 130 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 307 329 283 168 124 NC_009009:SSA_1940|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_III,_putative_1927129..1927359_NEGATIVE 306 357 318 50 10 NC_009009:SSA_1459|5end_RNA_methyltransferase,_putative_1467481..1467711_NEGATIVE 304 60 17 159 118 NC_009009:SSA_0535|5end_Propanediol_utilization:_dehydratase,_medium_subunit,_putative_530643..530873_POSITIVE 301 329 287 69 26 NC_009009:SSA_1617|5end_hypothetical_protein_1620651..1620881_NEGATIVE 301 417 373 83 39 NC_009009:SSA_0552|5end_Cof_family_protein,_putative_547424..547654_POSITIVE 300 49 2 59 9 NC_009009:SSA_1746|5end_hypothetical_protein_1732945..1733175_NEGATIVE 298 308 279 131 101 NC_009009:SSA_1910|5end_hypothetical_protein_1902672..1902902_NEGATIVE 298 49 1 208 161 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 296 430 384 216 162 NC_009009:SSA_1315|5end_hypothetical_protein_1332052..1332282_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 385 148 101 43 1 NC_009009:SSA_0521|3end_Ethanolamine_utilization_protein_EutL,_putative_521131..521281_POSITIVE 355 330 281 75 19 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 323 39 1 151 107 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 305 356 311 56 4 NC_009009:SSA_0057|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_61246..61396_POSITIVE 304 60 17 147 106 NC_009009:SSA_0533|3end_Glycerol_dehydratase_large_subunit_pduC,_putative_530711..530861_POSITIVE 300 49 2 66 16 NC_009009:SSA_1747|3end_hypothetical_protein_1732938..1733088_NEGATIVE 298 308 279 138 108 NC_009009:SSA_1911|3end_Conserved_uncharacterized_protein_1902665..1902815_NEGATIVE 298 439 391 77 19 NC_009009:SSA_1269|3end_hypothetical_protein_1291970..1292120_NEGATIVE 296 430 384 111 57 NC_009009:SSA_1316|3end_Nicotinamide_mononucleotide_transporter,_putative_1332157..1332307_NEGATIVE 294 50 1 115 76 NC_009009:SSA_0589|3end_Acetylornithine_deacetylase/succinyl-diaminopimelate_desuccinylase_(M20/M25/M40_family_peptidase),_putative_582207..582357_POSITIVE 290 330 285 148 95 NC_009009:SSA_1124|3end_Oxidoreductase,_putative_1148547..1148697_NEGATIVE 287 353 320 134 101 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 285 31 2 76 45 NC_009009:SSA_1015|3end_4-hydroxybenzoate_octaprenyltransferase,_putative_1019682..1019832_POSITIVE 280 47 2 82 30 NC_009009:SSA_1152|3end_Protein_chain_release_factor_A,_putative_1181918..1182068_POSITIVE 274 318 279 149 108 NC_009009:SSA_0661|3end_Isoleucyl-tRNA_synthetase,_putative_647748..647898_POSITIVE 273 129 82 117 81 NC_009009:SSA_1372|3end_hypothetical_protein_1388946..1389096_NEGATIVE 273 413 373 53 19 NC_009009:SSA_1130|3end_Iron-dependent_peroxidase,_putative_1157090..1157240_POSITIVE 273 353 319 56 23 NC_009009:SSA_0086|3end_V-type_sodium_ATPase,_subunit_K,_putative_88398..88548_POSITIVE 272 350 312 60 20 NC_009009:SSA_1061|3end_50S_ribosomal_protein_L21,_putative_1077986..1078136_POSITIVE 272 317 279 133 97 NC_009009:SSA_0401|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_399222..399372_POSITIVE