Origin IGS: tattattacttccttttcttgataatgaaatattttaacacaattctggaacaaaacaaagaatttgcttcgcttttactatcttttagcagtcaaaacatgagcagctagtgcaaatctcgtgttcctaaatatcaaataagccacactaagcccaatataaaaatagactagtttcactagtctatcatatctatctcataaagactaatatatttttcttatcacagcgataagaaaagtatatca .........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 tgatatacttttcttatcgctgtgataagaaaaatatattagtctttatgagatagatatgatagactagtgaaactagtctatttttatattgggcttagtgtggcttatttgatatttaggaacacgagatttgcactagctgctcatgttttgactgctaaaagatagtaaaagcgaagcaaattctttgttttgttccagaattgtgttaaaatatttcattatcaagaaaaggaagtaataata Mask Tandem Repeat Region ================================================ tattattacttccttttcttgataatgaaatattttaacacaattctggaacaaaacaaagaatttgcttcgcttttactatcttttagcagtcaaaacatgagcagctagtgcaaatctcgtgttcctaaatatcaaataagccacactaagcccaatataaaaatagactagtttcactagtctatcatatctatctcataaagactaatatatttttcttatcacagcgataagaaaagtatatca Find is-nt database================================================ Query_seq: SSA_1868:SSA_1869|SSA_1868:SSA_1869:ABC-type arginine/histidine transport system, permease component, putative:ATP-dependent RNA helicase, putative:<-<-:1863993..1864241 249 tattattacttccttttcttgataatgaaatattttaacacaattctggaacaaaacaaagaatttgcttcgcttttactatcttttagcagtcaaaacatgagcagctagtgcaaatctcgtgttcctaaatatcaaataagccacactaagcccaatataaaaatagactagtttcactagtctatcatatctatctcataaagactaatatatttttcttatcacagcgataagaaaagtatatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1868:SSA_1869|SSA_1868:SSA_1869:ABC-type arginine/histidine transport system, permease component, putative:ATP-dependent RNA helicase, putative:<-<-:1863993..1864241 249 tattattacttccttttcttgataatgaaatattttaacacaattctggaacaaaacaaagaatttgcttcgcttttactatcttttagcagtcaaaacatgagcagctagtgcaaatctcgtgttcctaaatatcaaataagccacactaagcccaatataaaaatagactagtttcactagtctatcatatctatctcataaagactaatatatttttcttatcacagcgataagaaaagtatatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1868:SSA_1869|SSA_1868:SSA_1869:ABC-type arginine/histidine transport system, permease component, putative:ATP-dependent RNA helicase, putative:<-<-:1863993..1864241 249 tattattacttccttttcttgataatgaaatattttaacacaattctggaacaaaacaaagaatttgcttcgcttttactatcttttagcagtcaaaacatgagcagctagtgcaaatctcgtgttcctaaatatcaaataagccacactaagcccaatataaaaatagactagtttcactagtctatcatatctatctcataaagactaatatatttttcttatcacagcgataagaaaagtatatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tattattacttccttttcttgataatgaaatattttaacacaattctggaacaaaacaaagaatttgcttcgcttttactatcttttagcagtcaaaacatgagcagctagtgcaaatctcgtgttcctaaatatcaaataagccacactaagcccaatataaaaatagactagtttcactagtctatcatatctatctcataaagactaatatatttttcttatcacagcgataagaaaagtatatca Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 19 End: 108 .................. M I M K Y F N T I L E Q N K E F A S L L L S F S S Q N M S S ............................................................................................................................................. Protein_Len: 33 Strand: - Start: 82 End: 180 ................................................................................. R K A T L V H A A L A F R T N R F I L Y A V S L G I Y F Y V L K M ..................................................................... tattattacttccttttcttgataatgaaatattttaacacaattctggaacaaaacaaagaatttgcttcgcttttactatcttttagcagtcaaaacatgagcagctagtgcaaatctcgtgttcctaaatatcaaataagccacactaagcccaatataaaaatagactagtttcactagtctatcatatctatctcataaagactaatatatttttcttatcacagcgataagaaaagtatatca 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================================================ tattattacttccttttcttgataatgaaatattttaacacaattctggaacaaaacaaagaatttgcttcgcttttactatcttttagcagtcaaaacatgagcagctagtgcaaatctcgtgttcctaaatatcaaataagccacactaagcccaatataaaaatagactagtttcactagtctatcatatctatctcataaagactaatatatttttcttatcacagcgataagaaaagtatatca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -11.3 Tail_Score: -5.09762 Start: 167 End: 187 Full_Region: atgagatagatatga tagactagt gaa actagtcta tttttatattgggct ......................................................................................................................................................................tagactagtgaaactagtcta.............................................................. Find igs database================================================ Query_seq: SSA_1868:SSA_1869|SSA_1868:SSA_1869:ABC-type arginine/histidine transport system, permease component, putative:ATP-dependent RNA helicase, putative:<-<-:1863993..1864241 249 tattattacttccttttcttgataatgaaatattttaacacaattctggaacaaaacaaagaatttgcttcgcttttactatcttttagcagtcaaaacatgagcagctagtgcaaatctcgtgttcctaaatatcaaataagccacactaagcccaatataaaaatagactagtttcactagtctatcatatctatctcataaagactaatatatttttcttatcacagcgataagaaaagtatatca Intra-Species Hit: Count: 1 Min: 1 Max: 249 Len: 249 Subject: NC_009009_SSA_1868_SSA_1869|ABC-type arginine/histidine transport system, permease component, putative:ATP-dependent RNA helicase, putative|NEGATIVE:NEGATIVE|[1863993,1864241]|249 HSP 1 e-value: 1.0E-139 bit: 494.0 Len: 249 Query Start:1 Query End:249 Subject Strand: POSITIVE Subject Start: 1 Subject End: 249 tattattacttccttttcttgataatgaaatattttaacacaattctggaacaaaacaaagaatttgcttcgcttttactatcttttagcagtcaaaacatgagcagctagtgcaaatctcgtgttcctaaatatcaaataagccacactaagcccaatataaaaatagactagtttcactagtctatcatatctatctcataaagactaatatatttttcttatcacagcgataagaaaagtatatca tattattacttccttttcttgataatgaaatattttaacacaattctggaacaaaacaaagaatttgcttcgcttttactatcttttagcagtcaaaacatgagcagctagtgcaaatctcgtgttcctaaatatcaaataagccacactaagcccaatataaaaatagactagtttcactagtctatcatatctatctcataaagactaatatatttttcttatcacagcgataagaaaagtatatca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUAUUACUUCCUUUUCUUGAUAAUGAAAUAUUUUAACACAAUUCUGGAACAAAACAAAGAAUUUGCUUCGCUUUUACUAUCUUUUAGCAGUCAAAACAUGAGCAGCUAGUGCAAAUCUCGUGUUCCUAAAUAUCAAAUAAGCCACACUAAGCCCAAUAUAAAAAUAGACUAGUUUCACUAGUCUAUCAUAUCUAUCUCAUAAAGACUAAUAUAUUUUUCUUAUCACAGCGAUAAGAAAAGUAUAUCA ............((((....((((((((....(((((.....(((..((((((......(((.(((((.................(((((.((((.....))).).))))).))))))))..))))))..))).........((........))......))))).((((((((.....))))))))))))...))))....))))....((((((((((((((((.....)))))))))))))))).. (-46.47) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUAUACUUUUCUUAUCGCUGUGAUAAGAAAAAUAUAUUAGUCUUUAUGAGAUAGAUAUGAUAGACUAGUGAAACUAGUCUAUUUUUAUAUUGGGCUUAGUGUGGCUUAUUUGAUAUUUAGGAACACGAGAUUUGCACUAGCUGCUCAUGUUUUGACUGCUAAAAGAUAGUAAAAGCGAAGCAAAUUCUUUGUUUUGUUCCAGAAUUGUGUUAAAAUAUUUCAUUAUCAAGAAAAGGAAGUAAUAAUA (((((((.((((((((((.....)))))))))).)))))))(((....((((...(((((((((((((((.....))))))))))...)))))...))))....)))...(((((((....((((((.(((....((....))..))).(((((((..(((((.....)))))....)))))))............)))))).(((.(((......))).)))..)))))))................. (-61.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 887 130 81 221 172 NC_009009:SSA_1868|5end_ABC-type_arginine/histidine_transport_system,_permease_component,_putative_1863902..1864132_NEGATIVE 290 108 63 140 92 NC_009009:SSA_1140|5end_Dihydrolipoamide_acetyl_transferase,_E2_component,_putative_1167868..1168098_POSITIVE 277 128 83 163 120 NC_009009:SSA_1087|5end_ABC-type_transporter_(antibiotic_resistance_protein),_ATPase_component,_putative_1104524..1104754_POSITIVE 268 148 101 160 105 NC_009009:SSA_2097|5end_Amino_acid_ABC_transporter,_ATP-binding_protein,_putative_2102918..2103148_NEGATIVE 262 129 100 45 17 NC_009009:SSA_0862|5end_MurM,_putative_854221..854451_NEGATIVE 261 130 81 146 90 NC_009009:SSA_1324|5end_Ceramide_glucosyltransferase,_putative_1341618..1341848_NEGATIVE 260 128 84 51 1 NC_009009:SSA_0688|5end_2,3-bisphosphoglycerate-dependent_phosphoglycerate_mutase,_putative_671360..671590_POSITIVE 257 108 68 71 26 NC_009009:SSA_0508|5end_Conserved_uncharacterized_protein,_possible_phosphoserine_phosphatase_506668..506898_POSITIVE 256 128 84 195 141 NC_009009:SSA_1013|5end_Phosphatidylserine_synthase,_putative_1017221..1017451_POSITIVE 255 118 71 187 128 NC_009009:SSA_1793|5end_Histidine_kinase_(sensor_protein),_putative_1776361..1776591_NEGATIVE 254 129 92 231 189 NC_009009:SSA_1649|5end_hypothetical_protein_1648886..1649116_NEGATIVE 254 128 85 169 114 NC_009009:SSA_0090|5end_Acetyltransferase,_GNAT_family,_putative_90258..90488_POSITIVE 251 130 85 175 123 NC_009009:SSA_1085|5end_Dihydrodipicolinate_reductase,_putative_1102564..1102794_POSITIVE 251 108 64 226 189 NC_009009:SSA_0239|5end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_232961..233191_POSITIVE 250 50 8 105 52 NC_009009:SSA_0393|5end_Bacteriocin_ABC-type_exporter,_ATP_binding/permease_protein,_putative_388766..388996_POSITIVE 248 129 82 173 114 NC_009009:SSA_1831|5end_hypothetical_protein_1821138..1821368_POSITIVE 248 130 87 180 136 NC_009009:SSA_0204|5end_Nisin_biosynthesis_two-component_response_transcriptional_regulator_nisR,_putative_202057..202287_POSITIVE 246 116 83 57 26 NC_009009:SSA_2207|5end_hypothetical_protein_2207221..2207451_NEGATIVE 246 145 101 225 182 NC_009009:SSA_0491|5end_Alpha-ribazole-5'-phosphate_phosphatase,_putative_490961..491191_POSITIVE 244 107 67 87 36 NC_009009:SSA_1137|5end_Dihydrolipoamide_dehydrogenase,_putative_1164375..1164605_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 290 108 63 126 78 NC_009009:SSA_1139|3end_Pyruvate_dehydrogenase_E1_component_beta_subunit,_putative_1167934..1168084_POSITIVE 268 148 101 147 92 NC_009009:SSA_2098|3end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2102931..2103081_NEGATIVE 262 129 100 60 32 NC_009009:SSA_0863|3end_Cof_family_protein,_putative_854206..854356_NEGATIVE 257 146 101 136 82 NC_009009:SSA_2201|3end_hypothetical_protein_2202237..2202387_POSITIVE 257 110 65 143 91 NC_009009:SSA_1496|3end_hypothetical_protein_1502473..1502623_NEGATIVE 257 90 57 142 108 NC_009009:SSA_0368|3end_hypothetical_protein_359722..359872_POSITIVE 254 98 57 112 70 NC_009009:SSA_2106|3end_Flavin_monoxygenase,_putative_2108015..2108165_NEGATIVE 251 130 85 134 82 NC_009009:SSA_1084|3end_Conserved_uncharacterized_protein_1102603..1102753_POSITIVE 248 109 61 150 110 NC_009009:SSA_1845|3end_Serine/threonine_protein_kinase,_putative_1838328..1838478_NEGATIVE 248 129 82 146 87 NC_009009:SSA_1830|3end_Aminoglycoside_phosphotransferase,_putative_1821191..1821341_POSITIVE 242 116 72 55 16 NC_009009:SSA_0057|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_61246..61396_POSITIVE 236 129 82 136 99 NC_009009:SSA_1911|3end_Conserved_uncharacterized_protein_1902665..1902815_NEGATIVE 234 227 182 66 21 NC_009009:SSA_0854|3end_hypothetical_protein_841813..841963_POSITIVE 233 109 64 137 101 NC_009009:SSA_0808|3end_hypothetical_protein_791012..791162_POSITIVE 231 90 44 147 111 NC_009009:SSA_2348|3end_Metal_dependent_hydrolase,_putative_2349875..2350025_NEGATIVE 231 120 71 148 104 NC_009009:SSA_1631|3end_Sortase-like_protein,_putative_1631651..1631801_NEGATIVE 231 130 81 134 73 NC_009009:SSA_1484|3end_DNA_ligase,_putative_1490230..1490380_NEGATIVE 230 129 81 143 101 NC_009009:SSA_0606|3end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_593789..593939_NEGATIVE 229 110 66 57 23 NC_009009:SSA_1403|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1416222..1416372_NEGATIVE 224 128 83 132 77 NC_009009:SSA_2081|3end_hypothetical_protein_2085490..2085640_POSITIVE