Origin IGS: tagacaccactctttctataataaaataaggaatgggagaaaaatcagcagactaggtcgtgattttatcatcccactcccaaaatacgaataatagttgattgagaaacgaagaagaatagattataaaacaatactctttcaaatccgtagatttataaagaaagaaatcatctactaacttgctcaagcaactagaaatagaaaacaagtcaaagactgggatagccccagcctcgtaacta .........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 tagttacgaggctggggctatcccagtctttgacttgttttctatttctagttgcttgagcaagttagtagatgatttctttctttataaatctacggatttgaaagagtattgttttataatctattcttcttcgtttctcaatcaactattattcgtattttgggagtgggatgataaaatcacgacctagtctgctgatttttctcccattccttattttattatagaaagagtggtgtcta Mask Tandem Repeat Region ================================================ tagacaccactctttctataataaaataaggaatgggagaaaaatcagcagactaggtcgtgattttatcatcccactcccaaaatacgaataatagttgattgagaaacgaagaagaatagattataaaacaatactctttcaaatccgtagatttataaagaaagaaatcatctactaacttgctcaagcaactagaaatagaaaacaagtcaaagactgggatagccccagcctcgtaacta Find is-nt database================================================ Query_seq: SSA_1728:SSA_1729|SSA_1728:SSA_1729:ABC transporter membrane-spanning permease-branched chain amino acid transport, putative:ABC transporter substrate-binding protein-branched chain amino acid transport, putative:<-<-:1714384..1714628 245 tagacaccactctttctataataaaataaggaatgggagaaaaatcagcagactaggtcgtgattttatcatcccactcccaaaatacgaataatagttgattgagaaacgaagaagaatagattataaaacaatactctttcaaatccgtagatttataaagaaagaaatcatctactaacttgctcaagcaactagaaatagaaaacaagtcaaagactgggatagccccagcctcgtaacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1728:SSA_1729|SSA_1728:SSA_1729:ABC transporter membrane-spanning permease-branched chain amino acid transport, putative:ABC transporter substrate-binding protein-branched chain amino acid transport, putative:<-<-:1714384..1714628 245 tagacaccactctttctataataaaataaggaatgggagaaaaatcagcagactaggtcgtgattttatcatcccactcccaaaatacgaataatagttgattgagaaacgaagaagaatagattataaaacaatactctttcaaatccgtagatttataaagaaagaaatcatctactaacttgctcaagcaactagaaatagaaaacaagtcaaagactgggatagccccagcctcgtaacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1728:SSA_1729|SSA_1728:SSA_1729:ABC transporter membrane-spanning permease-branched chain amino acid transport, putative:ABC transporter substrate-binding protein-branched chain amino acid transport, putative:<-<-:1714384..1714628 245 tagacaccactctttctataataaaataaggaatgggagaaaaatcagcagactaggtcgtgattttatcatcccactcccaaaatacgaataatagttgattgagaaacgaagaagaatagattataaaacaatactctttcaaatccgtagatttataaagaaagaaatcatctactaacttgctcaagcaactagaaatagaaaacaagtcaaagactgggatagccccagcctcgtaacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagacaccactctttctataataaaataaggaatgggagaaaaatcagcagactaggtcgtgattttatcatcccactcccaaaatacgaataatagttgattgagaaacgaagaagaatagattataaaacaatactctttcaaatccgtagatttataaagaaagaaatcatctactaacttgctcaagcaactagaaatagaaaacaagtcaaagactgggatagccccagcctcgtaacta Predict ORF larger than 30AA ================================================ Protein_Len: 57 Strand: - Start: 56 End: 226 ....................................................... T T I K D D W E W F V F L L Q N L F S S S Y I I F C Y E K L D T S K Y L F F D D V L K S L C S S I S F L D F V P M ................... Protein_Len: 34 Strand: - Start: 19 End: 120 .................. L L I L F P L F I L L S P R S K I M G S G F Y S Y Y N I S F R L L M ............................................................................................................................. tagacaccactctttctataataaaataaggaatgggagaaaaatcagcagactaggtcgtgattttatcatcccactcccaaaatacgaataatagttgattgagaaacgaagaagaatagattataaaacaatactctttcaaatccgtagatttataaagaaagaaatcatctactaacttgctcaagcaactagaaatagaaaacaagtcaaagactgggatagccccagcctcgtaacta 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: 82 Start: 101 End: 130 ....................................................................................................ATTGAGAAACGAAGAAGAATAGATTATAAA................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagacaccactctttctataataaaataaggaatgggagaaaaatcagcagactaggtcgtgattttatcatcccactcccaaaatacgaataatagttgattgagaaacgaagaagaatagattataaaacaatactctttcaaatccgtagatttataaagaaagaaatcatctactaacttgctcaagcaactagaaatagaaaacaagtcaaagactgggatagccccagcctcgtaacta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 78 HP_score: -6.6 Tail_Score: -4.49377 Start: 30 End: 80 Full_Region: attattcgtattttg ggagtgggatgataaaatcacgac cta gtctgctgatttttctcccattcc ttattttattataga .............................ggagtgggatgataaaatcacgacctagtctgctgatttttctcccattcc..................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_1728:SSA_1729|SSA_1728:SSA_1729:ABC transporter membrane-spanning permease-branched chain amino acid transport, putative:ABC transporter substrate-binding protein-branched chain amino acid transport, putative:<-<-:1714384..1714628 245 tagacaccactctttctataataaaataaggaatgggagaaaaatcagcagactaggtcgtgattttatcatcccactcccaaaatacgaataatagttgattgagaaacgaagaagaatagattataaaacaatactctttcaaatccgtagatttataaagaaagaaatcatctactaacttgctcaagcaactagaaatagaaaacaagtcaaagactgggatagccccagcctcgtaacta Intra-Species Hit: Count: 1 Min: 1 Max: 245 Len: 245 Subject: NC_009009_SSA_1728_SSA_1729|ABC transporter membrane-spanning permease-branched chain amino acid transport, putative:ABC transporter substrate-binding protein-branched chain amino acid transport, putative|NEGATIVE:NEGATIVE|[1714384,1714628]|245 HSP 1 e-value: 1.0E-136 bit: 486.0 Len: 245 Query Start:1 Query End:245 Subject Strand: POSITIVE Subject Start: 1 Subject End: 245 tagacaccactctttctataataaaataaggaatgggagaaaaatcagcagactaggtcgtgattttatcatcccactcccaaaatacgaataatagttgattgagaaacgaagaagaatagattataaaacaatactctttcaaatccgtagatttataaagaaagaaatcatctactaacttgctcaagcaactagaaatagaaaacaagtcaaagactgggatagccccagcctcgtaacta tagacaccactctttctataataaaataaggaatgggagaaaaatcagcagactaggtcgtgattttatcatcccactcccaaaatacgaataatagttgattgagaaacgaagaagaatagattataaaacaatactctttcaaatccgtagatttataaagaaagaaatcatctactaacttgctcaagcaactagaaatagaaaacaagtcaaagactgggatagccccagcctcgtaacta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGACACCACUCUUUCUAUAAUAAAAUAAGGAAUGGGAGAAAAAUCAGCAGACUAGGUCGUGAUUUUAUCAUCCCACUCCCAAAAUACGAAUAAUAGUUGAUUGAGAAACGAAGAAGAAUAGAUUAUAAAACAAUACUCUUUCAAAUCCGUAGAUUUAUAAAGAAAGAAAUCAUCUACUAACUUGCUCAAGCAACUAGAAAUAGAAAACAAGUCAAAGACUGGGAUAGCCCCAGCCUCGUAACUA ..(((.......(((((((..........(((.((((((((((((((...(((...))).))))))).)).))))).)))..............((((((.(((((......((.(((...((((............(((((((((((....))))).....)))))))))).))).))......))))).))))))...)))))))....)))..((.(((((.....))))).))........ (-52.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUUACGAGGCUGGGGCUAUCCCAGUCUUUGACUUGUUUUCUAUUUCUAGUUGCUUGAGCAAGUUAGUAGAUGAUUUCUUUCUUUAUAAAUCUACGGAUUUGAAAGAGUAUUGUUUUAUAAUCUAUUCUUCUUCGUUUCUCAAUCAACUAUUAUUCGUAUUUUGGGAGUGGGAUGAUAAAAUCACGACCUAGUCUGCUGAUUUUUCUCCCAUUCCUUAUUUUAUUAUAGAAAGAGUGGUGUCUA .(((((.(((((((((.....))))))))))))))..((((((((...((((((.(((((.(((..((((((((((....((((((.((((((....))))))))))))....))).....)))))))...))).....))))).)))))).............((((((((((.((.(((((((((((...))).).))))))))))))))))))).........))))))))........... (-69.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 913 80 31 171 122 NC_009009:SSA_1728|5end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1714293..1714523_NEGATIVE 294 74 31 65 31 NC_009009:SSA_2213|5end_Nucleotide_sugar_dehydratase,_putative_2215111..2215341_NEGATIVE 292 80 44 172 131 NC_009009:SSA_1617|5end_hypothetical_protein_1620651..1620881_NEGATIVE 291 235 191 231 192 NC_009009:SSA_0513|5end_ATP:cob(I)alamin_adenosyltransferase,_putative_511558..511788_POSITIVE 288 90 44 71 27 NC_009009:SSA_0204|5end_Nisin_biosynthesis_two-component_response_transcriptional_regulator_nisR,_putative_202057..202287_POSITIVE 287 236 197 185 142 NC_009009:SSA_0726|5end_FmtA-like_protein,_putative_710905..711135_POSITIVE 282 239 192 183 122 NC_009009:SSA_1574|5end_Glycosyl_transferase,_family_1,_putative_1577930..1578160_NEGATIVE 277 227 182 75 37 NC_009009:SSA_2099|5end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2104313..2104543_NEGATIVE 274 81 45 40 3 NC_009009:SSA_2304|5end_Conserved_uncharacterized_protein_2306270..2306500_NEGATIVE 274 236 209 60 20 NC_009009:SSA_0198|5end_Dihydrofolate_synthetase,_putative_196901..197131_POSITIVE 268 229 181 183 127 NC_009009:SSA_1323|5end_hypothetical_protein_1340450..1340680_NEGATIVE 266 90 46 98 42 NC_009009:SSA_1266|5end_crcB-like_protein_1,_putative_1291000..1291230_NEGATIVE 264 240 194 157 108 NC_009009:SSA_1800|5end_UDP-N-acetylmuramate--L-alanine_ligase,_putative_1782371..1782601_NEGATIVE 260 64 29 73 41 NC_009009:SSA_1000|5end_Galactose_operon_transcriptional_repressor,_LacI_family,_putative_1000734..1000964_NEGATIVE 258 237 195 47 3 NC_009009:SSA_0793|5end_DNA-entry_nuclease,_putative_774859..775089_POSITIVE 257 78 46 169 136 NC_009009:SSA_1776|5end_Potassium_uptake_protein,_Trk_family,_putative_1762639..1762869_POSITIVE 255 63 29 226 190 NC_009009:SSA_2092|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095975..2096205_NEGATIVE 255 240 218 209 187 NC_009009:SSA_1748|5end_Inorganic_pyrophosphatase/exopolyphosphatase,_putative_1734478..1734708_NEGATIVE 255 240 192 74 19 NC_009009:SSA_0069|5end_Hypothetical_protein,_possibly_membrane-associated_73037..73267_POSITIVE 252 237 195 147 101 NC_009009:SSA_1889|5end_Conserved_uncharacterized_protein_1887122..1887352_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 294 74 31 63 29 NC_009009:SSA_2214|3end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_2,_putative_2215113..2215263_NEGATIVE 292 80 44 103 62 NC_009009:SSA_1618|3end_hypothetical_protein_1620720..1620870_NEGATIVE 288 238 215 41 14 NC_009009:SSA_1409|3end_DTDP-glucose-4,6-dehydratase,_putative_1421209..1421359_NEGATIVE 288 90 44 58 14 NC_009009:SSA_0203|3end_hypothetical_protein_202124..202274_POSITIVE 277 230 181 63 14 NC_009009:SSA_1867|3end_ABC-type_polar_amino_acid_transport_system,_ATPase_component,_putative_1862353..1862503_NEGATIVE 275 240 207 89 56 NC_009009:SSA_0599|3end_hypothetical_protein_589007..589157_POSITIVE 274 236 209 58 18 NC_009009:SSA_0197|3end_Dihydropteroate_synthase,_putative_196979..197129_POSITIVE 266 90 46 125 69 NC_009009:SSA_1267|3end_crcB-like_protein_2,_putative_1290973..1291123_NEGATIVE 264 80 35 79 30 NC_009009:SSA_0379|3end_PTS_system,_beta-glucoside-specific_EII_component,_putative_370833..370983_POSITIVE 255 240 218 70 48 NC_009009:SSA_1749|3end_Pyruvate_formate-lyase-activating_enzyme,_putative_1734617..1734767_NEGATIVE 252 230 189 150 110 NC_009009:SSA_2170|3end_hypothetical_protein_2169557..2169707_NEGATIVE 252 237 213 83 55 NC_009009:SSA_1491|3end_Methionine_aminopeptidase_A,_putative_1496780..1496930_NEGATIVE 251 240 191 90 40 NC_009009:SSA_2332|3end_D-alanyl_carrier_protein,_putative_2334957..2335107_NEGATIVE 250 237 214 59 31 NC_009009:SSA_1705|3end_hypothetical_protein_1696398..1696548_NEGATIVE 248 107 61 130 78 NC_009009:SSA_0915|3end_hypothetical_protein_928014..928164_POSITIVE 244 236 191 146 99 NC_009009:SSA_2198|3end_hypothetical_protein_2197842..2197992_NEGATIVE 243 240 191 57 3 NC_009009:SSA_2309|3end_Fimbrial_assembly_protein,_putative_2310474..2310624_NEGATIVE 241 82 47 56 11 NC_009009:SSA_0475|3end_CbiK_protein,_putative_478570..478720_POSITIVE 240 89 48 121 86 NC_009009:SSA_0547|3end_Acyl_carrier_protein_synthase,_putative_542433..542583_POSITIVE 239 240 220 138 108 NC_009009:SSA_2223|3end_Capsular_polysaccharide_biosynthesis_protein_Wzd_(chain_length_regulator),_putative_2224008..2224158_NEGATIVE