Origin IGS: atcaataccagcctgagctagaaatgtctcgtaagcctgcctttgactagcaggcagcggctccgtgatttgaaacttatccgaggtctctagctgagcaggcctttgtgcaatctgacacccatctgccgggcaaagctgaaagccacataactacttttctatcttcaatatctttgccccctcttcattacaactaatagatctctgctaacattacttcaatttctatcggagaagttgttctaaaatctttaaaacaaagagataagcaaaatcattaaattgactcttttaatttctaatatgatataattatttaaaatatcatattagtgagaatattatgtcaaagacaaaaggtaataaaaaaagaaattcttctaaagtcaaatatatcttaggaagcggagctttaattttatcctctacagttcttctgcctagagtattgaaaaaaactagaaattatgtatataaaaaacaagtaacactagccaatcatctaaaaactagttttgatgggaaggacacgttagttaaaaaatctgactataacaaaggtagaagata .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tatcttctacctttgttatagtcagattttttaactaacgtgtccttcccatcaaaactagtttttagatgattggctagtgttacttgttttttatatacataatttctagtttttttcaatactctaggcagaagaactgtagaggataaaattaaagctccgcttcctaagatatatttgactttagaagaatttctttttttattaccttttgtctttgacataatattctcactaatatgatattttaaataattatatcatattagaaattaaaagagtcaatttaatgattttgcttatctctttgttttaaagattttagaacaacttctccgatagaaattgaagtaatgttagcagagatctattagttgtaatgaagagggggcaaagatattgaagatagaaaagtagttatgtggctttcagctttgcccggcagatgggtgtcagattgcacaaaggcctgctcagctagagacctcggataagtttcaaatcacggagccgctgcctgctagtcaaaggcaggcttacgagacatttctagctcaggctggtattgat Mask Tandem Repeat Region ================================================ atcaataccagcctgagctagaaatgtctcgtaagcctgcctttgactagcaggcagcggctccgtgatttgaaacttatccgaggtctctagctgagcaggcctttgtgcaatctgacacccatctgccgggcaaagctgaaagccacataactacttttctatcttcaatatctttgccccctcttcattacaactaatagatctctgctaacattacttcaatttctatcggagaagttgttctaaaatctttaaaacaaagagataagcaaaatcattaaattgactcttttaatttctaatatgatataattatttaaaatatcatattagtgagaatattatgtcaaagacaaaaggtaataaaaaaagaaattcttctaaagtcaaatatatcttaggaagcggagctttaattttatcctctacagttcttctgcctagagtattgaaaaaaactagaaattatgtatataaaaaacaagtaacactagccaatcatctaaaaactagttttgatgggaaggacacgttagttaaaaaatctgactataacaaaggtagaagata Find is-nt database================================================ Query_seq: SSA_2024:SSA_2025|SSA_2024:SSA_2025:hypothetical protein:Conserved hypothetical GTPase protein:<-->:2029363..2029935 573 atcaataccagcctgagctagaaatgtctcgtaagcctgcctttgactagcaggcagcggctccgtgatttgaaacttatccgaggtctctagctgagcaggcctttgtgcaatctgacacccatctgccgggcaaagctgaaagccacataactacttttctatcttcaatatctttgccccctcttcattacaactaatagatctctgctaacattacttcaatttctatcggagaagttgttctaaaatctttaaaacaaagagataagcaaaatcattaaattgactcttttaatttctaatatgatataattatttaaaatatcatattagtgagaatattatgtcaaagacaaaaggtaataaaaaaagaaattcttctaaagtcaaatatatcttaggaagcggagctttaattttatcctctacagttcttctgcctagagtattgaaaaaaactagaaattatgtatataaaaaacaagtaacactagccaatcatctaaaaactagttttgatgggaaggacacgttagttaaaaaatctgactataacaaaggtagaagata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2024:SSA_2025|SSA_2024:SSA_2025:hypothetical protein:Conserved hypothetical GTPase protein:<-->:2029363..2029935 573 atcaataccagcctgagctagaaatgtctcgtaagcctgcctttgactagcaggcagcggctccgtgatttgaaacttatccgaggtctctagctgagcaggcctttgtgcaatctgacacccatctgccgggcaaagctgaaagccacataactacttttctatcttcaatatctttgccccctcttcattacaactaatagatctctgctaacattacttcaatttctatcggagaagttgttctaaaatctttaaaacaaagagataagcaaaatcattaaattgactcttttaatttctaatatgatataattatttaaaatatcatattagtgagaatattatgtcaaagacaaaaggtaataaaaaaagaaattcttctaaagtcaaatatatcttaggaagcggagctttaattttatcctctacagttcttctgcctagagtattgaaaaaaactagaaattatgtatataaaaaacaagtaacactagccaatcatctaaaaactagttttgatgggaaggacacgttagttaaaaaatctgactataacaaaggtagaagata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2024:SSA_2025|SSA_2024:SSA_2025:hypothetical protein:Conserved hypothetical GTPase protein:<-->:2029363..2029935 573 atcaataccagcctgagctagaaatgtctcgtaagcctgcctttgactagcaggcagcggctccgtgatttgaaacttatccgaggtctctagctgagcaggcctttgtgcaatctgacacccatctgccgggcaaagctgaaagccacataactacttttctatcttcaatatctttgccccctcttcattacaactaatagatctctgctaacattacttcaatttctatcggagaagttgttctaaaatctttaaaacaaagagataagcaaaatcattaaattgactcttttaatttctaatatgatataattatttaaaatatcatattagtgagaatattatgtcaaagacaaaaggtaataaaaaaagaaattcttctaaagtcaaatatatcttaggaagcggagctttaattttatcctctacagttcttctgcctagagtattgaaaaaaactagaaattatgtatataaaaaacaagtaacactagccaatcatctaaaaactagttttgatgggaaggacacgttagttaaaaaatctgactataacaaaggtagaagata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 1 Max: 147 Len: 147 Subject: UniRef90_Q935V1 Cluster: Putative carboxylate-amine/thiol ligase; n=2; Streptococcus thermophilus|Rep: Putative carboxylate-amine/thiol ligase - Streptococcus thermophilus HSP 1 e-value: 7.0E-9 bit: 62.8 Len: 147 Query Start:1 Query End:147 Subject Strand: null Subject Start: 209 Subject End: 257 G F Q L C P A D G C Q I A Q R P A Q L E T S D K F Q I T E P L P A S Q R Q A Y E T F L A Q A G I D .......................................................................................................................................................................................................................................................................................................................................................................................................................................... G F Q L C P A D E C N I G S R S E Q L E T S N K F E I T D P L P L E L Q N M F E K F L N S A K I D .......................................................................................................................................................................................................................................................................................................................................................................................................................................... nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnacataactacttttctatcttcaatatctttgccccctcttcattacaactaatagatctctgctaacattacttcaatttctatcggagaagttgttctaaaatctttaaaacaaagagataagcaaaatcattaaattgactcttttaatttctaatatgatataattatttaaaatatcatattagtgagaatattatgtcaaagacaaaaggtaataaaaaaagaaattcttctaaagtcaaatatatcttaggaagcggagctttaattttatcctctacagttcttctgcctagagtattgaaaaaaactagaaattatgtatataaaaaacaagtaacactagccaatcatctaaaaactagttttgatgggaaggacacgttagttaaaaaatctgactataacaaaggtagaagata Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 108 End: 197 ........................................................................................................... M Q S D T H L P G K A E S H I T T F L S S I S L P P L H Y N ........................................................................................................................................................................................................................................................................................................................................................................................ Protein_Len: 60 Strand: + Start: 332 End: 571 ........................................................................................................................................................................................................................................................................................................................................... M S E N I M S K T K G N K K R N S S K V K Y I L G S G A L I L S S T V L L P R V L K K T R N Y V Y K K Q V T L A N H L K .. Protein_Len: 30 Strand: - Start: 331 End: 420 .......................................................................................................................................................................................................................................................................................................................................... I L S F I I D F V F P L L F L F E E L T L Y I K P L P A K M ......................................................................................................................................................... Protein_Len: 31 Strand: - Start: 80 End: 172 ............................................................................... G L D R A S C A K T C D S V W R G P L A S L W M V V K R D E M ................................................................................................................................................................................................................................................................................................................................................................................................................. Protein_Len: 38 Strand: - Start: 1 End: 114 D I G A Q A L F T E Y A Q R Q S A P L P E T I Q F K D S T E L Q A P R Q A M ........................................................................................................................................................................................................................................................................................................................................................................................................................................................................... nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnacataactacttttctatcttcaatatctttgccccctcttcattacaactaatagatctctgctaacattacttcaatttctatcggagaagttgttctaaaatctttaaaacaaagagataagcaaaatcattaaattgactcttttaatttctaatatgatataattatttaaaatatcatattagtgagaatattatgtcaaagacaaaaggtaataaaaaaagaaattcttctaaagtcaaatatatcttaggaagcggagctttaattttatcctctacagttcttctgcctagagtattgaaaaaaactagaaattatgtatataaaaaacaagtaacactagccaatcatctaaaaactagttttgatgggaaggacacgttagttaaaaaatctgactataacaaaggtagaagata 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: 81 Start: 365 End: 394 ............................................................................................................................................................................................................................................................................................................................................................................TTTGACTTTAGAAGAATTTCTTTTTTTATT................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnacataactacttttctatcttcaatatctttgccccctcttcattacaactaatagatctctgctaacattacttcaatttctatcggagaagttgttctaaaatctttaaaacaaagagataagcaaaatcattaaattgactcttttaatttctaatatgatataattatttaaaatatcatattagtgagaatattatgtcaaagacaaaaggtaataaaaaaagaaattcttctaaagtcaaatatatcttaggaagcggagctttaattttatcctctacagttcttctgcctagagtattgaaaaaaactagaaattatgtatataaaaaacaagtaacactagccaatcatctaaaaactagttttgatgggaaggacacgttagttaaaaaatctgactataacaaaggtagaagata Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 55 HP_score: -4.8 Tail_Score: -3.38218 Start: 223 End: 243 Full_Region: CTGCTAACATTACTT CAATTTCT ATCGG AGAAGTTG TTCTAAAATCTTTAA ..............................................................................................................................................................................................................................CAATTTCTATCGGAGAAGTTG.......................................................................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_2024:SSA_2025|SSA_2024:SSA_2025:hypothetical protein:Conserved hypothetical GTPase protein:<-->:2029363..2029935 573 nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnacataactacttttctatcttcaatatctttgccccctcttcattacaactaatagatctctgctaacattacttcaatttctatcggagaagttgttctaaaatctttaaaacaaagagataagcaaaatcattaaattgactcttttaatttctaatatgatataattatttaaaatatcatattagtgagaatattatgtcaaagacaaaaggtaataaaaaaagaaattcttctaaagtcaaatatatcttaggaagcggagctttaattttatcctctacagttcttctgcctagagtattgaaaaaaactagaaattatgtatataaaaaacaagtaacactagccaatcatctaaaaactagttttgatgggaaggacacgttagttaaaaaatctgactataacaaaggtagaagata Intra-Species Hit: Count: 1 Min: 148 Max: 573 Len: 426 Subject: NC_009009_SSA_2024_SSA_2025|hypothetical protein:Conserved hypothetical GTPase protein|NEGATIVE:POSITIVE|[2029363,2029935]|573 HSP 1 e-value: 0.0 bit: 761.0 Len: 426 Query Start:148 Query End:573 Subject Strand: POSITIVE Subject Start: 148 Subject End: 573 ...................................................................................................................................................acataactacttttctatcttcaatatctttgccccctcttcattacaactaatagatctctgctaacattacttcaatttctatcggagaagttgttctaaaatctttaaaacaaagagataagcaaaatcattaaattgactcttttaatttctaatatgatataattatttaaaatatcatattagtgagaatattatgtcaaagacaaaaggtaatnnnnnnngaaattcttctaaagtcaaatatatcttaggaagcggagctttaattttatcctctacagttcttctgcctagagtattgnnnnnnnctagaaattatgtatataaaaaacaagtaacactagccaatcatctaaaaactagttttgatgggaaggacacgttagttaaaaaatctgactataacaaaggtagaagata ...................................................................................................................................................acataactacttttctatcttcaatatctttgccccctcttcattacaactaatagatctctgctaacattacttcaatttctatcggagaagttgttctaaaatctttaaaacaaagagataagcaaaatcattaaattgactcttttaatttctaatatgatataattatttaaaatatcatattagtgagaatattatgtcaaagacaaaaggtaataaaaaaagaaattcttctaaagtcaaatatatcttaggaagcggagctttaattttatcctctacagttcttctgcctagagtattgaaaaaaactagaaattatgtatataaaaaacaagtaacactagccaatcatctaaaaactagttttgatgggaaggacacgttagttaaaaaatctgactataacaaaggtagaagata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAUAACUACUUUUCUAUCUUCAAUAUCUUUGCCCCCUCUUCAUUACAACUAAUAGAUCUCUGCUAACAUUACUUCAAUUUCUAUCGGAGAAGUUGUUCUAAAAUCUUUAAAACAAAGAGAUAAGCAAAAUCAUUAAAUUGACUCUUUUAAUUUCUAAUAUGAUAUAAUUAUUUAAAAUAUCAUAUUAGUGAGAAUAUUAUGUCAAAGACAAAAGGUAAUAAAAAAAGAAAUUCUUCUAAAGUCAAAUAUAUCUUAGGAAGCGGAGCUUUAAUUUUAUCCUCUACAGUUCUUCUGCCUAGAGUAUUGAAAAAAACUAGAAAUUAUGUAUAUAAAAAACAAGUAACACUAGCCAAUCAUCUAAAAACUAGUUUUGAUGGGAAGGACACGUUAGUUAAAAAAUCUGACUAUAACAAAGGUAGAAGAUA ...............(((((((..((((((((...(((..((((((.(((((.(((((....((((...((((...((((((((..((((((....((((...((((((.......))))))................(((((........((.((((((((((((...........)))))))))))).)).........)))))....................)))).)))))).....(((...((((..((((.((.((((((.((...........)).)))))).)).))))..))))))).......)))))))).(((.........))).))))...)))).....))))).....))))).))))))..)))....(((((.........))))).....))))))))))))))) (-80.83) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUCUUCUACCUUUGUUAUAGUCAGAUUUUUUAACUAACGUGUCCUUCCCAUCAAAACUAGUUUUUAGAUGAUUGGCUAGUGUUACUUGUUUUUUAUAUACAUAAUUUCUAGUUUUUUUCAAUACUCUAGGCAGAAGAACUGUAGAGGAUAAAAUUAAAGCUCCGCUUCCUAAGAUAUAUUUGACUUUAGAAGAAUUUCUUUUUUUAUUACCUUUUGUCUUUGACAUAAUAUUCUCACUAAUAUGAUAUUUUAAAUAAUUAUAUCAUAUUAGAAAUUAAAAGAGUCAAUUUAAUGAUUUUGCUUAUCUCUUUGUUUUAAAGAUUUUAGAACAACUUCUCCGAUAGAAAUUGAAGUAAUGUUAGCAGAGAUCUAUUAGUUGUAAUGAAGAGGGGGCAAAGAUAUUGAAGAUAGAAAAGUAGUUAUGU ..(((((((..........((((((((.(((((.......(((((((......((((((((...(((.((((..(((.((.....)).)))..)))).....)))...))))))))..............((((.....)))).)))))))......((((...))))..)))))...)))))))).)))))))............(((((.(((((((.(((((............((((((((((((...........))))))))))))...........))))).((((((.((((((((.((((((..(((((((((((((..(((((((((.............)))))..))))....))))))).))))....))..)))))))))))))).)))))).)))))))..)))))..... (-84.52) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 277 300 253 181 126 NC_009009:SSA_0204|5end_Nisin_biosynthesis_two-component_response_transcriptional_regulator_nisR,_putative_202057..202287_POSITIVE 272 304 265 224 186 NC_009009:SSA_1770|5end_hypothetical_protein_1758431..1758661_NEGATIVE 265 110 61 68 19 NC_009009:SSA_1944|5end_Oligopeptide_transport_ATP-binding_protein,_putative_1936611..1936841_NEGATIVE 262 297 253 186 141 NC_009009:SSA_1993|5end_Conserved_uncharacterized_protein_1990790..1991020_NEGATIVE 261 308 262 62 8 NC_009009:SSA_0996|5end_cGMP-specific_phosphodiesterase,_putative_996282..996512_POSITIVE 260 306 261 123 82 NC_009009:SSA_1121|5end_Cytochrome_C-type_biogenesis_protein,_putative_1147149..1147379_POSITIVE 257 64 27 230 190 NC_009009:SSA_1402|5end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_1416220..1416450_NEGATIVE 256 285 241 171 123 NC_009009:SSA_1368|5end_hypothetical_protein_1384077..1384307_NEGATIVE 253 297 255 115 75 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 252 304 262 203 168 NC_009009:SSA_1505|5end_hypothetical_protein_1509555..1509785_NEGATIVE 252 297 251 225 171 NC_009009:SSA_0142|5end_hypothetical_protein_137230..137460_POSITIVE 249 295 252 148 102 NC_009009:SSA_2097|5end_Amino_acid_ABC_transporter,_ATP-binding_protein,_putative_2102918..2103148_NEGATIVE 248 299 252 201 139 NC_009009:SSA_2007|5end_Chaperone_protein_dnaK/HSP70,_putative_2009272..2009502_NEGATIVE 247 307 261 41 2 NC_009009:SSA_1278|5end_Rhodanese-like_domain_protein,_putative_1299877..1300107_NEGATIVE 247 300 257 82 27 NC_009009:SSA_1229|5end_hypothetical_protein_1252421..1252651_NEGATIVE 247 300 257 206 151 NC_009009:SSA_1227|5end_Aminoglycoside_adenylyltransferase,_putative_1252297..1252527_NEGATIVE 247 310 263 141 81 NC_009009:SSA_0972|5end_hypothetical_protein_979973..980203_POSITIVE 247 303 261 125 81 NC_009009:SSA_0316|5end_hypothetical_protein_310576..310806_POSITIVE 246 296 252 60 8 NC_009009:SSA_2309|5end_Fimbrial_assembly_protein,_putative_2311886..2312116_NEGATIVE 246 61 22 126 89 NC_009009:SSA_1896|5end_Translation_initiation_factor_IF-2,_putative_1894134..1894364_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 286 108 72 134 96 NC_009009:SSA_0597|3end_hypothetical_protein_588563..588713_POSITIVE 279 270 226 151 106 NC_009009:SSA_0506|3end_Iron-sulfur_cluster-binding_protein,_putative_504430..504580_NEGATIVE 279 89 41 122 67 NC_009009:SSA_0373|3end_Dihydroorotate_dehydrogenase,_putative_363080..363230_POSITIVE 270 307 263 133 84 NC_009009:SSA_0413|3end_Anthranilate/para-aminobenzoate_synthases_component_I/_Chorismate_binding_enzyme,_putative_408315..408465_NEGATIVE 265 110 61 57 8 NC_009009:SSA_1945|3end_Oligopeptide_transport_ATP-binding_protein,_putative_1936622..1936772_NEGATIVE 262 297 253 115 70 NC_009009:SSA_1994|3end_CTP_synthase,_putative_1990861..1991011_NEGATIVE 262 297 257 120 76 NC_009009:SSA_0249|3end_hypothetical_protein_242115..242265_POSITIVE 260 298 251 148 93 NC_009009:SSA_1024|3end_Alpha-amylase,_putative_1041182..1041332_NEGATIVE 256 285 241 106 58 NC_009009:SSA_1369|3end_FmtA-like_protein,_putative_1384142..1384292_NEGATIVE 253 63 28 112 64 NC_009009:SSA_0825|3end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_805056..805206_POSITIVE 253 297 255 118 78 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 252 297 251 106 52 NC_009009:SSA_0141|3end_Copper_chaperone,_putative_137191..137341_POSITIVE 249 295 252 135 89 NC_009009:SSA_2098|3end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2102931..2103081_NEGATIVE 248 298 252 101 53 NC_009009:SSA_0686|3end_Fe2+/Zn2+_uptake_regulation_protein,_putative_670079..670229_POSITIVE 247 307 261 48 9 NC_009009:SSA_1279|3end_Oxidoreductase,_putative_1299870..1300020_NEGATIVE 247 303 261 115 71 NC_009009:SSA_0315|3end_Transcriptional_regulator,_MarR_family,_putative_310646..310796_POSITIVE 246 61 22 106 69 NC_009009:SSA_1897|3end_Ribosomal_protein_HS6-type_(S12/L30/L7a),_putative_1894154..1894304_NEGATIVE 238 60 11 132 79 NC_009009:SSA_1255|3end_hypothetical_protein_1281456..1281606_NEGATIVE 236 319 275 136 91 NC_009009:SSA_1496|3end_hypothetical_protein_1502473..1502623_NEGATIVE 236 268 232 122 83 NC_009009:SSA_1138|3end_Pyruvate_dehydrogenase,_TPP-dependent_E1_component_alpha-subunit,_putative_1166884..1167034_POSITIVE