Origin IGS: ggtctttctcctcttcttccaaacttcatttttagatactccctattttacacctttttaagatattttcaagtattattttcaattttcagaaaattttgttattcaatcttctttgccactatcaaacttttagaaattggaaaaaccagctcgtgcgaactggtttgatga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcatcaaaccagttcgcacgagctggtttttccaatttctaaaagtttgatagtggcaaagaagattgaataacaaaattttctgaaaattgaaaataatacttgaaaatatcttaaaaaggtgtaaaatagggagtatctaaaaatgaagtttggaagaagaggagaaagacc Mask Tandem Repeat Region ================================================ ggtctttctcctcttcttccaaacttcatttttagatactccctattttacacctttttaagatattttcaagtattattttcaattttcagaaaattttgttattcaatcttctttgccactatcaaacttttagaaattggaaaaaccagctcgtgcgaactggtttgatga Find is-nt database================================================ Query_seq: SSA_1225:SSA_1226|SSA_1225:SSA_1226:Branched-chain amino acid aminotransferase, putative:ParC, putative:<-<-:1248699..1248872 174 ggtctttctcctcttcttccaaacttcatttttagatactccctattttacacctttttaagatattttcaagtattattttcaattttcagaaaattttgttattcaatcttctttgccactatcaaacttttagaaattggaaaaaccagctcgtgcgaactggtttgatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1225:SSA_1226|SSA_1225:SSA_1226:Branched-chain amino acid aminotransferase, putative:ParC, putative:<-<-:1248699..1248872 174 ggtctttctcctcttcttccaaacttcatttttagatactccctattttacacctttttaagatattttcaagtattattttcaattttcagaaaattttgttattcaatcttctttgccactatcaaacttttagaaattggaaaaaccagctcgtgcgaactggtttgatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1225:SSA_1226|SSA_1225:SSA_1226:Branched-chain amino acid aminotransferase, putative:ParC, putative:<-<-:1248699..1248872 174 ggtctttctcctcttcttccaaacttcatttttagatactccctattttacacctttttaagatattttcaagtattattttcaattttcagaaaattttgttattcaatcttctttgccactatcaaacttttagaaattggaaaaaccagctcgtgcgaactggtttgatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggtctttctcctcttcttccaaacttcatttttagatactccctattttacacctttttaagatattttcaagtattattttcaattttcagaaaattttgttattcaatcttctttgccactatcaaacttttagaaattggaaaaaccagctcgtgcgaactggtttgatga Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 28 End: 168 ........................... M F R Y S L F Y T F L R Y F Q V L F S I F R K F C Y S I F F A T I K L L E I G K T S S C E L V ...... Protein_Len: 46 Strand: + Start: 36 End: 173 ................................... M L P I L H L F K I F S S I I F N F Q K I L L F N L L C H Y Q T F R N W K N Q L V R T G L M . ggtctttctcctcttcttccaaacttcatttttagatactccctattttacacctttttaagatattttcaagtattattttcaattttcagaaaattttgttattcaatcttctttgccactatcaaacttttagaaattggaaaaaccagctcgtgcgaactggtttgatga 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================================================ ggtctttctcctcttcttccaaacttcatttttagatactccctattttacacctttttaagatattttcaagtattattttcaattttcagaaaattttgttattcaatcttctttgccactatcaaacttttagaaattggaaaaaccagctcgtgcgaactggtttgatga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1225:SSA_1226|SSA_1225:SSA_1226:Branched-chain amino acid aminotransferase, putative:ParC, putative:<-<-:1248699..1248872 174 ggtctttctcctcttcttccaaacttcatttttagatactccctattttacacctttttaagatattttcaagtattattttcaattttcagaaaattttgttattcaatcttctttgccactatcaaacttttagaaattggaaaaaccagctcgtgcgaactggtttgatga Intra-Species Hit: Count: 1 Min: 1 Max: 174 Len: 174 Subject: NC_009009_SSA_1225_SSA_1226|Branched-chain amino acid aminotransferase, putative:ParC, putative|NEGATIVE:NEGATIVE|[1248699,1248872]|174 HSP 1 e-value: 8.0E-30 bit: 131.0 Len: 66 Query Start:109 Query End:174 Subject Strand: POSITIVE Subject Start: 109 Subject End: 174 ............................................................................................................atcttctttgccactatcaaacttttagaaattggaaaaaccagctcgtgcgaactggtttgatga ............................................................................................................atcttctttgccactatcaaacttttagaaattggaaaaaccagctcgtgcgaactggtttgatga HSP 2 e-value: 2.0E-6 bit: 54.0 Len: 27 Query Start:1 Query End:27 Subject Strand: POSITIVE Subject Start: 1 Subject End: 27 ggtctttctcctcttcttccaaacttc................................................................................................................................................... ggtctttctcctcttcttccaaacttc................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUCUUUCUCCUCUUCUUCCAAACUUCAUUUUUAGAUACUCCCUAUUUUACACCUUUUUAAGAUAUUUUCAAGUAUUAUUUUCAAUUUUCAGAAAAUUUUGUUAUUCAAUCUUCUUUGCCACUAUCAAACUUUUAGAAAUUGGAAAAACCAGCUCGUGCGAACUGGUUUGAUGA ((.......))..............(((((....((((((...(((((((........)))))))......))))))..((((((((((...((((.((((.....(((......))).......)))).)))).)))))))))).((((((.((....)).)))))).))))) (-22.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAUCAAACCAGUUCGCACGAGCUGGUUUUUCCAAUUUCUAAAAGUUUGAUAGUGGCAAAGAAGAUUGAAUAACAAAAUUUUCUGAAAAUUGAAAAUAAUACUUGAAAAUAUCUUAAAAAGGUGUAAAAUAGGGAGUAUCUAAAAAUGAAGUUUGGAAGAAGAGGAGAAAGACC ......(((((((((....)))))))))(((((..((((((((.((((..(((..((..((((((((.........)))))))).................((((...((((((.....))))))....))))..))..))).))))....))))))))....)))))...... (-33.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 799 50 1 141 92 NC_009009:SSA_1225|5end_Branched-chain_amino_acid_aminotransferase,_putative_1248608..1248838_NEGATIVE 339 48 5 140 91 NC_009009:SSA_2217|5end_Cps9H,_putative_2219045..2219275_NEGATIVE 279 44 5 106 58 NC_009009:SSA_0734|5end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_716895..717125_POSITIVE 254 38 9 133 97 NC_009009:SSA_0388|5end_Mismatch_repair_ATPase_(MutS_family),_putative_382474..382704_POSITIVE 250 159 111 144 100 NC_009009:SSA_2044|5end_Cysteinyl-tRNA_synthetase,_putative_2048409..2048639_NEGATIVE 248 168 123 66 16 NC_009009:SSA_1410|5end_DTDP-4-keto-6-deoxyglucose-3,5-epimerase,_putative_1423086..1423316_NEGATIVE 240 160 111 62 3 NC_009009:SSA_1488|5end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_1494657..1494887_NEGATIVE 239 46 2 55 14 NC_009009:SSA_1736|5end_L-cysteine_desulfhydrase,_putative_1722619..1722849_NEGATIVE 239 32 3 214 187 NC_009009:SSA_1250|5end_Conserved_uncharacterized_protein,_putative_1274512..1274742_NEGATIVE 237 38 2 135 94 NC_009009:SSA_0849|5end_Signal_peptidase_I,_putative_836127..836357_POSITIVE 234 41 2 85 47 NC_009009:SSA_1835|5end_Late_competence_protein,_putative_1830941..1831171_NEGATIVE 234 39 2 128 92 NC_009009:SSA_0343|5end_DNA-damage-inducible_protein_P,_putative_337525..337755_POSITIVE 233 21 5 117 101 NC_009009:SSA_1013|5end_Phosphatidylserine_synthase,_putative_1017221..1017451_POSITIVE 232 53 11 132 96 NC_009009:SSA_0315|5end_Transcriptional_regulator,_MarR_family,_putative_310102..310332_POSITIVE 231 40 1 57 11 NC_009009:SSA_0674|5end_Exodeoxyribonuclease_VII_large_subunit,_putative_657071..657301_POSITIVE 229 167 134 56 18 NC_009009:SSA_0323|5end_Flavoprotein,_putative_316799..317029_NEGATIVE 228 154 111 47 2 NC_009009:SSA_1592|5end_hypothetical_protein_1596397..1596627_NEGATIVE 228 127 86 74 30 NC_009009:SSA_0671|5end_Methylenetetrahydrofolate_dehydrogenase/methenyltetrahydrofolate_cyclohydrolase,_putative_654340..654570_POSITIVE 227 168 121 228 180 NC_009009:SSA_2313|5end_hypothetical_protein_2315848..2316078_NEGATIVE 227 44 4 123 82 NC_009009:SSA_1821|5end_Acetyltransferase_(N-acetylase_of_ribosomal_proteins),_putative_1810610..1810840_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 339 48 5 62 13 NC_009009:SSA_2218|3end_Glycosyltransferase_(cell_wall_biogenesis)_Cps9G,_putative_2219123..2219273_NEGATIVE 279 44 5 68 20 NC_009009:SSA_0733|3end_hypothetical_protein_716937..717087_POSITIVE 272 169 123 79 33 NC_009009:SSA_0571|3end_Aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_B,_putative_566894..567044_POSITIVE 269 169 131 84 43 NC_009009:SSA_1557|3end_SRPR,_signal_recognition_particle-docking_protein,_putative_1558502..1558652_NEGATIVE 261 47 9 147 104 NC_009009:SSA_0214|3end_Single-strand_DNA-binding_protein_(conjugal_DNA-protein_transfer_system),_putative_210690..210840_POSITIVE 255 167 130 82 44 NC_009009:SSA_1041|3end_Sugar_ABC_transporter,_permease_protein,_putative_1057434..1057584_POSITIVE 255 43 3 131 95 NC_009009:SSA_1020|3end_hypothetical_protein_1036104..1036254_POSITIVE 254 42 9 127 94 NC_009009:SSA_0994|3end_Peptidase_E,_putative_995390..995540_POSITIVE 250 159 111 126 82 NC_009009:SSA_2045|3end_Reductase,_putative_2048427..2048577_NEGATIVE 248 168 123 61 11 NC_009009:SSA_1411|3end_Glucose-1-phosphate_thymidylytransferase,_putative_1423091..1423241_NEGATIVE 247 120 78 129 89 NC_009009:SSA_1211|3end_hypothetical_protein_1235344..1235494_POSITIVE 246 55 11 137 99 NC_009009:SSA_1256|3end_NAD-dependent_deacetylase,_putative_1282357..1282507_NEGATIVE 239 46 2 53 12 NC_009009:SSA_1737|3end_Cystathionine_gamma-synthase,_putative_1722621..1722771_NEGATIVE 234 41 2 88 50 NC_009009:SSA_1836|3end_Superfamily_II_ATP-dependent_DNA/RNA_helicase_required_for_DNA_uptake_(late_competence_protein),_putative_1830938..1831088_NEGATIVE 234 42 3 148 104 NC_009009:SSA_1717|3end_Modification_methylase_DpnIIB,_putative_1704155..1704305_NEGATIVE 233 21 5 130 114 NC_009009:SSA_1012|3end_Phosphoenolpyruvate_synthase,_putative_1017314..1017464_POSITIVE 231 40 1 147 105 NC_009009:SSA_1382|3end_hypothetical_protein_1399797..1399947_NEGATIVE 229 42 3 150 108 NC_009009:SSA_0906|3end_CshA-like_fibrillar_surface_protein_C_917411..917561_POSITIVE 228 154 111 54 9 NC_009009:SSA_1593|3end_Dipeptidase,_putative_1596390..1596540_NEGATIVE 226 45 1 116 67 NC_009009:SSA_0063|3end_Holliday_junction_DNA_helicase_ruvB,_putative_66413..66563_POSITIVE