Origin IGS: caagcaagaaaaagactgattaggccccaacctattcagtctttttagtacatactcttgcgccaaccggctttcaaatgatagatagtcgctataaaaatcactgataaaacaatcaaactattctttaaaagaaattaaaaaaattaatattccagaaaatacaatactaataattgacaagaccaagaccctaatctcgtttaaatctgtgtacaaagaataaagaaaaatgagtaaattaagcaaaatcactgatctataaaacctagattggctctgcttccatccttttaaagtatgaaaagcaaatggaaatctcaaaccgaatccagcatttctagaaggaaaaaaatggtttaagcccaaaagaaaaaatgcaacaatagcaatccataatgaaatcatgacagtcatccacctttctatctttgcacttcagacacaaaaggaaacatttt .........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 aaaatgtttccttttgtgtctgaagtgcaaagatagaaaggtggatgactgtcatgatttcattatggattgctattgttgcattttttcttttgggcttaaaccatttttttccttctagaaatgctggattcggtttgagatttccatttgcttttcatactttaaaaggatggaagcagagccaatctaggttttatagatcagtgattttgcttaatttactcatttttctttattctttgtacacagatttaaacgagattagggtcttggtcttgtcaattattagtattgtattttctggaatattaatttttttaatttcttttaaagaatagtttgattgttttatcagtgatttttatagcgactatctatcatttgaaagccggttggcgcaagagtatgtactaaaaagactgaataggttggggcctaatcagtctttttcttgcttg Mask Tandem Repeat Region ================================================ caagcaagaaaaagactgattaggccccaacctattcagtctttttagtacatactcttgcgccaaccggctttcaaatgatagatagtcgctataaaaatcactgataaaacaatcaaactattctttaaaagaaattaaaaaaattaatattccagaaaatacaatactaataattgacaagaccaagaccctaatctcgtttaaatctgtgtacaaagaataaagaaaaatgagtaaattaagcaaaatcactgatctataaaacctagattggctctgcttccatccttttaaagtatgaaaagcaaatggaaatctcaaaccgaatccagcatttctagaaggaaaaaaatggtttaagcccaaaagaaaaaatgcaacaatagcaatccataatgaaatcatgacagtcatccacctttctatctttgcacttcagacacaaaaggaaacatttt Find is-nt database================================================ Query_seq: SSA_1349:SSA_1350|SSA_1349:SSA_1350:Transcriptional regulator, biotin repressor family, putative:hypothetical protein:-><-:1366574..1367034 461 caagcaagaaaaagactgattaggccccaacctattcagtctttttagtacatactcttgcgccaaccggctttcaaatgatagatagtcgctataaaaatcactgataaaacaatcaaactattctttaaaagaaattaaaaaaattaatattccagaaaatacaatactaataattgacaagaccaagaccctaatctcgtttaaatctgtgtacaaagaataaagaaaaatgagtaaattaagcaaaatcactgatctataaaacctagattggctctgcttccatccttttaaagtatgaaaagcaaatggaaatctcaaaccgaatccagcatttctagaaggaaaaaaatggtttaagcccaaaagaaaaaatgcaacaatagcaatccataatgaaatcatgacagtcatccacctttctatctttgcacttcagacacaaaaggaaacatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1349:SSA_1350|SSA_1349:SSA_1350:Transcriptional regulator, biotin repressor family, putative:hypothetical protein:-><-:1366574..1367034 461 caagcaagaaaaagactgattaggccccaacctattcagtctttttagtacatactcttgcgccaaccggctttcaaatgatagatagtcgctataaaaatcactgataaaacaatcaaactattctttaaaagaaattaaaaaaattaatattccagaaaatacaatactaataattgacaagaccaagaccctaatctcgtttaaatctgtgtacaaagaataaagaaaaatgagtaaattaagcaaaatcactgatctataaaacctagattggctctgcttccatccttttaaagtatgaaaagcaaatggaaatctcaaaccgaatccagcatttctagaaggaaaaaaatggtttaagcccaaaagaaaaaatgcaacaatagcaatccataatgaaatcatgacagtcatccacctttctatctttgcacttcagacacaaaaggaaacatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1349:SSA_1350|SSA_1349:SSA_1350:Transcriptional regulator, biotin repressor family, putative:hypothetical protein:-><-:1366574..1367034 461 caagcaagaaaaagactgattaggccccaacctattcagtctttttagtacatactcttgcgccaaccggctttcaaatgatagatagtcgctataaaaatcactgataaaacaatcaaactattctttaaaagaaattaaaaaaattaatattccagaaaatacaatactaataattgacaagaccaagaccctaatctcgtttaaatctgtgtacaaagaataaagaaaaatgagtaaattaagcaaaatcactgatctataaaacctagattggctctgcttccatccttttaaagtatgaaaagcaaatggaaatctcaaaccgaatccagcatttctagaaggaaaaaaatggtttaagcccaaaagaaaaaatgcaacaatagcaatccataatgaaatcatgacagtcatccacctttctatctttgcacttcagacacaaaaggaaacatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caagcaagaaaaagactgattaggccccaacctattcagtctttttagtacatactcttgcgccaaccggctttcaaatgatagatagtcgctataaaaatcactgataaaacaatcaaactattctttaaaagaaattaaaaaaattaatattccagaaaatacaatactaataattgacaagaccaagaccctaatctcgtttaaatctgtgtacaaagaataaagaaaaatgagtaaattaagcaaaatcactgatctataaaacctagattggctctgcttccatccttttaaagtatgaaaagcaaatggaaatctcaaaccgaatccagcatttctagaaggaaaaaaatggtttaagcccaaaagaaaaaatgcaacaatagcaatccataatgaaatcatgacagtcatccacctttctatctttgcacttcagacacaaaaggaaacatttt Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 104 End: 223 ....................................................................................................... M I K Q S N Y S L K E I K K I N I P E N T I L I I D K T K T L I S F K S V Y K E .............................................................................................................................................................................................................................................. Protein_Len: 35 Strand: - Start: 344 End: 448 ....................................................................................................................................................................................................................................................................................................................................................... F S F F P K L G F S F I C C Y C D M I F D H C D D V K R D K C K L C M ............. Protein_Len: 60 Strand: - Start: 124 End: 429 ........................................................................................................................... I V S R Y F R S Q S Q K W G K L T H F A F P F R L G F G A N R S P F F H N L G L L F F A V I A I W L S I M V T M W R E M ................................ Protein_Len: 36 Strand: - Start: 1 End: 108 L C S F S Q N P G L R N L R K L V Y E Q A L R S E F S L Y D S Y F D S M ................................................................................................................................................................................................................................................................................................................................................................. caagcaagaaaaagactgattaggccccaacctattcagtctttttagtacatactcttgcgccaaccggctttcaaatgatagatagtcgctataaaaatcactgataaaacaatcaaactattctttaaaagaaattaaaaaaattaatattccagaaaatacaatactaataattgacaagaccaagaccctaatctcgtttaaatctgtgtacaaagaataaagaaaaatgagtaaattaagcaaaatcactgatctataaaacctagattggctctgcttccatccttttaaagtatgaaaagcaaatggaaatctcaaaccgaatccagcatttctagaaggaaaaaaatggtttaagcccaaaagaaaaaatgcaacaatagcaatccataatgaaatcatgacagtcatccacctttctatctttgcacttcagacacaaaaggaaacatttt 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================================================ caagcaagaaaaagactgattaggccccaacctattcagtctttttagtacatactcttgcgccaaccggctttcaaatgatagatagtcgctataaaaatcactgataaaacaatcaaactattctttaaaagaaattaaaaaaattaatattccagaaaatacaatactaataattgacaagaccaagaccctaatctcgtttaaatctgtgtacaaagaataaagaaaaatgagtaaattaagcaaaatcactgatctataaaacctagattggctctgcttccatccttttaaagtatgaaaagcaaatggaaatctcaaaccgaatccagcatttctagaaggaaaaaaatggtttaagcccaaaagaaaaaatgcaacaatagcaatccataatgaaatcatgacagtcatccacctttctatctttgcacttcagacacaaaaggaaacatttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1349:SSA_1350|SSA_1349:SSA_1350:Transcriptional regulator, biotin repressor family, putative:hypothetical protein:-><-:1366574..1367034 461 caagcaagaaaaagactgattaggccccaacctattcagtctttttagtacatactcttgcgccaaccggctttcaaatgatagatagtcgctataaaaatcactgataaaacaatcaaactattctttaaaagaaattaaaaaaattaatattccagaaaatacaatactaataattgacaagaccaagaccctaatctcgtttaaatctgtgtacaaagaataaagaaaaatgagtaaattaagcaaaatcactgatctataaaacctagattggctctgcttccatccttttaaagtatgaaaagcaaatggaaatctcaaaccgaatccagcatttctagaaggaaaaaaatggtttaagcccaaaagaaaaaatgcaacaatagcaatccataatgaaatcatgacagtcatccacctttctatctttgcacttcagacacaaaaggaaacatttt Intra-Species Hit: Count: 1 Min: 1 Max: 461 Len: 461 Subject: NC_009009_SSA_1349_SSA_1350|Transcriptional regulator, biotin repressor family, putative:hypothetical protein|POSITIVE:NEGATIVE|[1366574,1367034]|461 HSP 1 e-value: 0.0 bit: 831.0 Len: 461 Query Start:1 Query End:461 Subject Strand: POSITIVE Subject Start: 1 Subject End: 461 caagcaagaaaaagactgattaggccccaacctattcagtctttttagtacatactcttgcgccaaccggctttcaaatgatagatagtcgctataaaaatcactgataaaacaatcaaactattctttaaaagaaattnnnnnnnttaatattccagaaaatacaatactaataattgacaagaccaagaccctaatctcgtttaaatctgtgtacaaagaataaagaaaaatgagtaaattaagcaaaatcactgatctataaaacctagattggctctgcttccatccttttaaagtatgaaaagcaaatggaaatctcaaaccgaatccagcatttctagaaggnnnnnnntggtttaagcccaaaagaaaaaatgcaacaatagcaatccataatgaaatcatgacagtcatccacctttctatctttgcacttcagacacaaaaggaaacatttt caagcaagaaaaagactgattaggccccaacctattcagtctttttagtacatactcttgcgccaaccggctttcaaatgatagatagtcgctataaaaatcactgataaaacaatcaaactattctttaaaagaaattaaaaaaattaatattccagaaaatacaatactaataattgacaagaccaagaccctaatctcgtttaaatctgtgtacaaagaataaagaaaaatgagtaaattaagcaaaatcactgatctataaaacctagattggctctgcttccatccttttaaagtatgaaaagcaaatggaaatctcaaaccgaatccagcatttctagaaggaaaaaaatggtttaagcccaaaagaaaaaatgcaacaatagcaatccataatgaaatcatgacagtcatccacctttctatctttgcacttcagacacaaaaggaaacatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAGCAAGAAAAAGACUGAUUAGGCCCCAACCUAUUCAGUCUUUUUAGUACAUACUCUUGCGCCAACCGGCUUUCAAAUGAUAGAUAGUCGCUAUAAAAAUCACUGAUAAAACAAUCAAACUAUUCUUUAAAAGAAAUUAAAAAAAUUAAUAUUCCAGAAAAUACAAUACUAAUAAUUGACAAGACCAAGACCCUAAUCUCGUUUAAAUCUGUGUACAAAGAAUAAAGAAAAAUGAGUAAAUUAAGCAAAAUCACUGAUCUAUAAAACCUAGAUUGGCUCUGCUUCCAUCCUUUUAAAGUAUGAAAAGCAAAUGGAAAUCUCAAACCGAAUCCAGCAUUUCUAGAAGGAAAAAAAUGGUUUAAGCCCAAAAGAAAAAAUGCAACAAUAGCAAUCCAUAAUGAAAUCAUGACAGUCAUCCACCUUUCUAUCUUUGCACUUCAGACACAAAAGGAAACAUUUU ...((((((((((((((((.((((......)))).))))))))))..........))))))(((....)))...((((.((((((.((..(((((.........((((......)))).....((((((....((((((((.....))))).)))...........................((((((..........(((((((...(((.(((.......))).))).)))))))......(((((......(..(((((.......)))))..)...)))))...((((((((......((((.((...((((..((.......)).)))))).))))))))))))......)))))).......))))))...........)))))........(((....))).............)).))))))))))................(....)..... (-79.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUGUUUCCUUUUGUGUCUGAAGUGCAAAGAUAGAAAGGUGGAUGACUGUCAUGAUUUCAUUAUGGAUUGCUAUUGUUGCAUUUUUUCUUUUGGGCUUAAACCAUUUUUUUCCUUCUAGAAAUGCUGGAUUCGGUUUGAGAUUUCCAUUUGCUUUUCAUACUUUAAAAGGAUGGAAGCAGAGCCAAUCUAGGUUUUAUAGAUCAGUGAUUUUGCUUAAUUUACUCAUUUUUCUUUAUUCUUUGUACACAGAUUUAAACGAGAUUAGGGUCUUGGUCUUGUCAAUUAUUAGUAUUGUAUUUUCUGGAAUAUUAAUUUUUUUAAUUUCUUUUAAAGAAUAGUUUGAUUGUUUUAUCAGUGAUUUUUAUAGCGACUAUCUAUCAUUUGAAAGCCGGUUGGCGCAAGAGUAUGUACUAAAAAGACUGAAUAGGUUGGGGCCUAAUCAGUCUUUUUCUUGCUUG ..........((((((((((....(((((((((.(((((((((..(((...(((((((...)))))))...((....((..(...........(((.......)))..........(((((((((.(((((((.(((((..(.((((((((..(((((........)))))))))))))).))))))))))))))))).))))...)..))...)).....)))..)))))))))....))))))))).((((((...((((((((((....)))))))))).....(((((((((.((.....)).)))))))))((((((((......)))))))).))))))...(((((...((((((....((((...))))..))))))..))))).....))))))))))...(((..(((((((((((.(((((....))))).)))))))))))..)))... (-114.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 311 70 22 195 148 NC_009009:SSA_1256|5end_NAD-dependent_deacetylase,_putative_1283094..1283324_NEGATIVE 303 75 38 123 86 NC_009009:SSA_1937|5end_Malonyl-CoA:ACP_transacylase,_putative_1924771..1925001_NEGATIVE 300 348 326 229 207 NC_009009:SSA_0997|5end_DNA-directed_DNA_polymerase_III_chain,_putative_996779..997009_POSITIVE 299 67 23 184 135 NC_009009:SSA_0031|5end_Glutamine_phosphoribosylpyrophosphate_amidotransferase,_putative_36439..36669_POSITIVE 297 110 61 228 172 NC_009009:SSA_1192|5end_hypothetical_protein_1219034..1219264_NEGATIVE 292 93 54 227 183 NC_009009:SSA_0017|5end_Cell_shape_determining_protein_MreC,_putative_22811..23041_POSITIVE 291 75 35 136 95 NC_009009:SSA_1438|5end_Acetyltransferase,_putative_1443612..1443842_NEGATIVE 288 438 393 150 106 NC_009009:SSA_1450|5end_hypothetical_protein_1452710..1452940_NEGATIVE 288 94 60 57 27 NC_009009:SSA_0588|5end_L-cystine_ABC_transporter,_substrate-binding_component,_putative_579800..580030_POSITIVE 287 316 271 174 137 NC_009009:SSA_2015|5end_Phosphoglycerate_mutase,_putative_2015492..2015722_NEGATIVE 285 85 42 187 145 NC_009009:SSA_1521|5end_Phosphoenolpyruvate_carboxylase,_putative_1530683..1530913_NEGATIVE 281 76 39 211 169 NC_009009:SSA_1822|5end_hypothetical_protein_1811125..1811355_NEGATIVE 277 73 35 214 178 NC_009009:SSA_1835|5end_Late_competence_protein,_putative_1830941..1831171_NEGATIVE 277 93 54 88 31 NC_009009:SSA_0786|5end_Proton-translocating_ATPase,_F1_sector,_alpha_subunit,_putative_768737..768967_POSITIVE 275 451 412 64 19 NC_009009:SSA_0749|5end_Competence_protein,_putative_730668..730898_POSITIVE 274 78 31 71 23 NC_009009:SSA_0457|5end_Fructokinase,_putative_460663..460893_POSITIVE 273 70 22 202 155 NC_009009:SSA_1955|5end_ABC-type_Fe-S_cluster_assembly_transporter,_permease_component,_putative_1952602..1952832_NEGATIVE 273 39 2 223 185 NC_009009:SSA_0674|5end_Exodeoxyribonuclease_VII_large_subunit,_putative_657071..657301_POSITIVE 271 71 31 48 3 NC_009009:SSA_1442|5end_Imidazole_glycerol-phosphate_synthase_subunit_hisF,_putative_1445941..1446171_NEGATIVE 266 350 305 106 49 NC_009009:SSA_1709|5end_hypothetical_protein_1698414..1698644_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 75 38 130 93 NC_009009:SSA_1938|3end_Enoyl-acyl_carrier_protein(ACP)_reductase,_putative_1924764..1924914_NEGATIVE 299 67 23 89 40 NC_009009:SSA_0030|3end_Phosphoribosylformylglycinamidine_synthase,_putative_36424..36574_POSITIVE 298 49 3 52 2 NC_009009:SSA_2101|3end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2104509..2104659_NEGATIVE 291 75 35 124 83 NC_009009:SSA_1439|3end_hypothetical_protein_1443624..1443774_NEGATIVE 288 438 393 116 72 NC_009009:SSA_1451|3end_Exonuclease_RexA,_putative_1452744..1452894_NEGATIVE 287 316 271 74 37 NC_009009:SSA_2016|3end_Phosphoglycerate_mutase,_putative_2015592..2015742_NEGATIVE 286 46 9 82 45 NC_009009:SSA_1349|3end_Transcriptional_regulator,_biotin_repressor_family,_putative_1366513..1366663_POSITIVE 285 85 42 140 98 NC_009009:SSA_1522|3end_Cell_division_protein_FtsW,_putative_1530730..1530880_NEGATIVE 285 315 271 54 11 NC_009009:SSA_0502|3end_Peptide_ABC_transporter,_permease_protein,_putative_502323..502473_POSITIVE 273 39 2 66 28 NC_009009:SSA_0673|3end_hypothetical_protein_656994..657144_POSITIVE 271 337 292 59 18 NC_009009:SSA_2345|3end_hypothetical_protein_2347502..2347652_POSITIVE 268 440 396 83 33 NC_009009:SSA_1672|3end_hypothetical_protein_1670291..1670441_NEGATIVE 264 88 47 65 22 NC_009009:SSA_1443|3end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1445944..1446094_NEGATIVE 263 45 3 66 32 NC_009009:SSA_0779|3end_Glycogen_phosphorylase,_putative_764685..764835_POSITIVE 261 33 2 82 51 NC_009009:SSA_1729|3end_ABC_transporter_substrate-binding_protein-branched_chain_amino_acid_transport,_putative_1714539..1714689_NEGATIVE 261 94 54 76 27 NC_009009:SSA_1130|3end_Iron-dependent_peroxidase,_putative_1157090..1157240_POSITIVE 255 68 22 130 68 NC_009009:SSA_1558|3end_Hydrolase,_HAD_superfamily_1560044..1560194_NEGATIVE 254 440 392 120 59 NC_009009:SSA_1725|3end_Branched-chain_amino_acid_ABC_transporter,_ATP-binding_protein,_putative_1710993..1711143_NEGATIVE 254 293 252 40 3 NC_009009:SSA_1080|3end_Transcriptional_repressor_of_the_fructose_operon,_DeoR_family,_putative_1098361..1098511_POSITIVE 254 66 21 138 101 NC_009009:SSA_0083|3end_hypothetical_protein_85840..85990_POSITIVE