Origin IGS: agaaatgtccccccttaaataaattgttatagagttacaaagtactgatagaaagaactaccaccttatcgggactatataacttcttcattataccataatttacgataccactccctttttttaaaaaaagaacaagatatagattaaaactataccttgttaagctccattcattcttggaagttaaccaacctatccagactaaataacaaaataaaaacataaagagaagatatagtttagcaccaaattttcttctg .........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 cagaagaaaatttggtgctaaactatatcttctctttatgtttttattttgttatttagtctggataggttggttaacttccaagaatgaatggagcttaacaaggtatagttttaatctatatcttgttctttttttaaaaaaagggagtggtatcgtaaattatggtataatgaagaagttatatagtcccgataaggtggtagttctttctatcagtactttgtaactctataacaatttatttaaggggggacatttct Mask Tandem Repeat Region ================================================ agaaatgtccccccttaaataaattgttatagagttacaaagtactgatagaaagaactaccaccttatcgggactatataacttcttcattataccataatttacgataccactccctttttttaaaaaaagaacaagatatagattaaaactataccttgttaagctccattcattcttggaagttaaccaacctatccagactaaataacaaaataaaaacataaagagaagatatagtttagcaccaaattttcttctg Find is-nt database================================================ Query_seq: SSA_1495:SSA_1496|SSA_1495:SSA_1496:S-adenosylmethionine synthetase, putative:hypothetical protein:<-<-:1502300..1502562 263 agaaatgtccccccttaaataaattgttatagagttacaaagtactgatagaaagaactaccaccttatcgggactatataacttcttcattataccataatttacgataccactccctttttttaaaaaaagaacaagatatagattaaaactataccttgttaagctccattcattcttggaagttaaccaacctatccagactaaataacaaaataaaaacataaagagaagatatagtttagcaccaaattttcttctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1495:SSA_1496|SSA_1495:SSA_1496:S-adenosylmethionine synthetase, putative:hypothetical protein:<-<-:1502300..1502562 263 agaaatgtccccccttaaataaattgttatagagttacaaagtactgatagaaagaactaccaccttatcgggactatataacttcttcattataccataatttacgataccactccctttttttaaaaaaagaacaagatatagattaaaactataccttgttaagctccattcattcttggaagttaaccaacctatccagactaaataacaaaataaaaacataaagagaagatatagtttagcaccaaattttcttctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1495:SSA_1496|SSA_1495:SSA_1496:S-adenosylmethionine synthetase, putative:hypothetical protein:<-<-:1502300..1502562 263 agaaatgtccccccttaaataaattgttatagagttacaaagtactgatagaaagaactaccaccttatcgggactatataacttcttcattataccataatttacgataccactccctttttttaaaaaaagaacaagatatagattaaaactataccttgttaagctccattcattcttggaagttaaccaacctatccagactaaataacaaaataaaaacataaagagaagatatagtttagcaccaaattttcttctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agaaatgtccccccttaaataaattgttatagagttacaaagtactgatagaaagaactaccaccttatcgggactatataacttcttcattataccataatttacgataccactccctttttttaaaaaaagaacaagatatagattaaaactataccttgttaagctccattcattcttggaagttaaccaacctatccagactaaataacaaaataaaaacataaagagaagatatagtttagcaccaaattttcttctg Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 108 End: 209 ........................................................................................................... M P L P F F K K R T R Y R L K L Y L V K L H S F L E V N Q P I Q T K ...................................................... Protein_Len: 60 Strand: - Start: 38 End: 226 ..................................... I S L V V V K D P S Y L K K M I G Y N V I G S G K K L F L V L Y L N F S Y R T L S W E N K S T L W G I W V L Y C F L F M ..................................... agaaatgtccccccttaaataaattgttatagagttacaaagtactgatagaaagaactaccaccttatcgggactatataacttcttcattataccataatttacgataccactccctttttttaaaaaaagaacaagatatagattaaaactataccttgttaagctccattcattcttggaagttaaccaacctatccagactaaataacaaaataaaaacataaagagaagatatagtttagcaccaaattttcttctg 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================================================ agaaatgtccccccttaaataaattgttatagagttacaaagtactgatagaaagaactaccaccttatcgggactatataacttcttcattataccataatttacgataccactccctttttttaaaaaaagaacaagatatagattaaaactataccttgttaagctccattcattcttggaagttaaccaacctatccagactaaataacaaaataaaaacataaagagaagatatagtttagcaccaaattttcttctg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 85 HP_score: -5.7 Tail_Score: -5.40072 Start: 133 End: 165 Full_Region: agaatgaatggagct taacaaggtatagtt tta atctatatcttgttc tttttttaaaaaaag ....................................................................................................................................taacaaggtatagttttaatctatatcttgttc.................................................................................................. TransTerm Strand: - Conf: 82 HP_score: -7.4 Tail_Score: -4.79949 Start: 136 End: 162 Full_Region: atgaatggagcttaa caaggtatagtt tta atctatatcttg ttctttttttaaaaa .......................................................................................................................................caaggtatagttttaatctatatcttg..................................................................................................... Find igs database================================================ Query_seq: SSA_1495:SSA_1496|SSA_1495:SSA_1496:S-adenosylmethionine synthetase, putative:hypothetical protein:<-<-:1502300..1502562 263 agaaatgtccccccttaaataaattgttatagagttacaaagtactgatagaaagaactaccaccttatcgggactatataacttcttcattataccataatttacgataccactccctttttttaaaaaaagaacaagatatagattaaaactataccttgttaagctccattcattcttggaagttaaccaacctatccagactaaataacaaaataaaaacataaagagaagatatagtttagcaccaaattttcttctg Intra-Species Hit: Count: 1 Min: 1 Max: 263 Len: 263 Subject: NC_009009_SSA_1495_SSA_1496|S-adenosylmethionine synthetase, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1502300,1502562]|263 HSP 1 e-value: 2.0E-68 bit: 260.0 Len: 131 Query Start:133 Query End:263 Subject Strand: POSITIVE Subject Start: 133 Subject End: 263 ....................................................................................................................................gaacaagatatagattaaaactataccttgttaagctccattcattcttggaagttaaccaacctatccagactaaataacaaaataaaaacataaagagaagatatagtttagcaccaaattttcttctg ....................................................................................................................................gaacaagatatagattaaaactataccttgttaagctccattcattcttggaagttaaccaacctatccagactaaataacaaaataaaaacataaagagaagatatagtttagcaccaaattttcttctg HSP 2 e-value: 1.0E-60 bit: 234.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 agaaatgtccccccttaaataaattgttatagagttacaaagtactgatagaaagaactaccaccttatcgggactatataacttcttcattataccataatttacgataccactccc................................................................................................................................................. agaaatgtccccccttaaataaattgttatagagttacaaagtactgatagaaagaactaccaccttatcgggactatataacttcttcattataccataatttacgataccactccc................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAAUGUCCCCCCUUAAAUAAAUUGUUAUAGAGUUACAAAGUACUGAUAGAAAGAACUACCACCUUAUCGGGACUAUAUAACUUCUUCAUUAUACCAUAAUUUACGAUACCACUCCCUUUUUUUAAAAAAAGAACAAGAUAUAGAUUAAAACUAUACCUUGUUAAGCUCCAUUCAUUCUUGGAAGUUAACCAACCUAUCCAGACUAAAUAACAAAAUAAAAACAUAAAGAGAAGAUAUAGUUUAGCACCAAAUUUUCUUCUG .......................(((((((..((((....(((.(((((((..............))))))).)))...((((((((..............................((((((....))))))((((((.(((((.......))))).)))))).................)))))))).............))))..)))))))...............((((((...(((((......))))).)))))). (-38.34) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGAAGAAAAUUUGGUGCUAAACUAUAUCUUCUCUUUAUGUUUUUAUUUUGUUAUUUAGUCUGGAUAGGUUGGUUAACUUCCAAGAAUGAAUGGAGCUUAACAAGGUAUAGUUUUAAUCUAUAUCUUGUUCUUUUUUUAAAAAAAGGGAGUGGUAUCGUAAAUUAUGGUAUAAUGAAGAAGUUAUAUAGUCCCGAUAAGGUGGUAGUUCUUUCUAUCAGUACUUUGUAACUCUAUAACAAUUUAUUUAAGGGGGGACAUUUCU ....(((((...((((.....))))..(((((((((...(((.((((...(((((..((((((.(((((..((...(((.((.....((((..(((...((((((((((((.......)))))))))))))))..))))......((((.((((((((((...))))))))...............)).)))).....)).)))...))..)))))))).)))..)))))...)))).)))......)))))))))..))))) (-59.26) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 842 80 31 171 122 NC_009009:SSA_1495|5end_S-adenosylmethionine_synthetase,_putative_1502209..1502439_NEGATIVE 311 206 169 220 168 NC_009009:SSA_1656|5end_Nisin_resistance_protein,_putative_1652890..1653120_NEGATIVE 245 89 44 161 111 NC_009009:SSA_2347|5end_Coenzyme_F390_synthetase,_putative_2349939..2350169_NEGATIVE 242 47 6 140 93 NC_009009:SSA_0993|5end_hypothetical_protein_994064..994294_POSITIVE 239 66 23 62 14 NC_009009:SSA_1409|5end_DTDP-glucose-4,6-dehydratase,_putative_1422255..1422485_NEGATIVE 237 94 58 36 1 NC_009009:SSA_1695|5end_Transcriptional_antiterminator,_BglG/SacY_family_(induction_of_sugar_metabolism),_putative_1688010..1688240_NEGATIVE 230 183 153 45 16 NC_009009:SSA_0037|5end_Phosphoribosylamine-glycine_ligase;_phosphoribosyl_glycinamide_synthetase_(GARS),_putative_44272..44502_POSITIVE 229 123 81 103 51 NC_009009:SSA_2217|5end_Cps9H,_putative_2219045..2219275_NEGATIVE 228 206 167 153 125 NC_009009:SSA_1550|5end_hypothetical_protein_1552665..1552895_NEGATIVE 227 210 165 85 36 NC_009009:SSA_0647|5end_hypothetical_protein_630998..631228_POSITIVE 227 90 42 111 57 NC_009009:SSA_0565|5end_hypothetical_protein_557230..557460_POSITIVE 224 193 151 56 15 NC_009009:SSA_0616|5end_YlbN-like_protein,_putative_609245..609475_POSITIVE 221 182 158 67 37 NC_009009:SSA_2226|5end_Organic_radical_activating_chaperone,_putative_2227756..2227986_NEGATIVE 221 85 56 63 38 NC_009009:SSA_1679|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_1673049..1673279_NEGATIVE 217 74 31 74 33 NC_009009:SSA_1638|5end_hypothetical_protein_1641325..1641555_NEGATIVE 217 104 61 104 48 NC_009009:SSA_0877|5end_Phosphoglycolate_phosphatase,_putative_871008..871238_POSITIVE 215 207 166 144 101 NC_009009:SSA_0977|5end_3-isopropylmalate_dehydrogenase,_putative_982771..983001_POSITIVE 215 189 158 74 30 NC_009009:SSA_0628|5end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_617892..618122_POSITIVE 214 87 46 209 175 NC_009009:SSA_1139|5end_Pyruvate_dehydrogenase_E1_component_beta_subunit,_putative_1166823..1167053_POSITIVE 214 134 103 117 75 NC_009009:SSA_0075|5end_ABC_sugar_transporter,_permease_protein,_putative_78963..79193_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 311 206 169 148 96 NC_009009:SSA_1657|3end_hypothetical_protein_1652962..1653112_NEGATIVE 260 201 165 103 69 NC_009009:SSA_0686|3end_Fe2+/Zn2+_uptake_regulation_protein,_putative_670079..670229_POSITIVE 250 193 159 112 76 NC_009009:SSA_1166|3end_hypothetical_protein_1192350..1192500_POSITIVE 242 47 6 143 96 NC_009009:SSA_0992|3end_hypothetical_protein_994147..994297_POSITIVE 227 210 165 83 34 NC_009009:SSA_0646|3end_hypothetical_protein_631076..631226_POSITIVE 224 206 166 45 2 NC_009009:SSA_2101|3end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2104509..2104659_NEGATIVE 221 182 158 107 77 NC_009009:SSA_2227|3end_Acetyl_transferase,_putative_2227716..2227866_NEGATIVE 221 76 31 79 40 NC_009009:SSA_1435|3end_hypothetical_protein_1441751..1441901_NEGATIVE 217 74 31 60 19 NC_009009:SSA_1639|3end_5'-methylthioadenosine/S-adenosylhomocysteine_nucleosidase,_putative_1641339..1641489_NEGATIVE 215 207 166 62 19 NC_009009:SSA_0975|3end_2-isopropylmalate_synthase,_putative_982769..982919_POSITIVE 215 189 158 77 33 NC_009009:SSA_0627|3end_hypothetical_protein_617975..618125_POSITIVE 214 134 103 49 7 NC_009009:SSA_0074|3end_ABC_transporter_substrate-binding_protein-sugar_transport,_putative_78975..79125_POSITIVE 213 184 142 131 94 NC_009009:SSA_2328|3end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_2332309..2332459_POSITIVE 213 206 169 56 13 NC_009009:SSA_0468|3end_Precorrin-6y_C5,15-methyltransferase-like,_putative_472418..472568_POSITIVE 212 76 31 75 31 NC_009009:SSA_1326|3end_Peptidase_T,_putative_1343735..1343885_POSITIVE 212 183 142 146 98 NC_009009:SSA_0807|3end_GTP-binding_protein,_putative_790839..790989_POSITIVE 211 150 101 60 9 NC_009009:SSA_0081|3end_Transcriptional_regulator,_RpiR_family_(phosphosugar-binding),_putative_84220..84370_NEGATIVE 210 206 168 99 51 NC_009009:SSA_2048|3end_Serine_acetyltransferase,_putative_2049984..2050134_NEGATIVE 208 200 153 106 54 NC_009009:SSA_1015|3end_4-hydroxybenzoate_octaprenyltransferase,_putative_1019682..1019832_POSITIVE 205 98 51 55 13 NC_009009:SSA_1784|3end_Glutamate_racemase,_putative_1769103..1769253_NEGATIVE