Origin IGS: attttaacacaatcttgccacttgtcaagcatttatgttatactatacaaaaaagatagtttgctaatcaaattattttttagattttattttggaggttgagct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agctcaacctccaaaataaaatctaaaaaataatttgattagcaaactatcttttttgtatagtataacataaatgcttgacaagtggcaagattgtgttaaaat Mask Tandem Repeat Region ================================================ attttaacacaatcttgccacttgtcaagcatttatgttatactatacaaaaaagatagtttgctaatcaaattattttttagattttattttggaggttgagct Find is-nt database================================================ Query_seq: SSA_1670:SSA_1671|SSA_1670:SSA_1671:Transcriptional regulator, TetR/AcrR family, putative:hypothetical protein:<-->:1669339..1669443 105 attttaacacaatcttgccacttgtcaagcatttatgttatactatacaaaaaagatagtttgctaatcaaattattttttagattttattttggaggttgagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1670:SSA_1671|SSA_1670:SSA_1671:Transcriptional regulator, TetR/AcrR family, putative:hypothetical protein:<-->:1669339..1669443 105 attttaacacaatcttgccacttgtcaagcatttatgttatactatacaaaaaagatagtttgctaatcaaattattttttagattttattttggaggttgagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1670:SSA_1671|SSA_1670:SSA_1671:Transcriptional regulator, TetR/AcrR family, putative:hypothetical protein:<-->:1669339..1669443 105 attttaacacaatcttgccacttgtcaagcatttatgttatactatacaaaaaagatagtttgctaatcaaattattttttagattttattttggaggttgagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attttaacacaatcttgccacttgtcaagcatttatgttatactatacaaaaaagatagtttgctaatcaaattattttttagattttattttggaggttgagct Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 1 End: 99 M L T Q S C H L S S I Y V I L Y K K D S L L I K L F F R F Y F G G ...... attttaacacaatcttgccacttgtcaagcatttatgttatactatacaaaaaagatagtttgctaatcaaattattttttagattttattttggaggttgagct 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================================================ attttaacacaatcttgccacttgtcaagcatttatgttatactatacaaaaaagatagtttgctaatcaaattattttttagattttattttggaggttgagct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1670:SSA_1671|SSA_1670:SSA_1671:Transcriptional regulator, TetR/AcrR family, putative:hypothetical protein:<-->:1669339..1669443 105 attttaacacaatcttgccacttgtcaagcatttatgttatactatacaaaaaagatagtttgctaatcaaattattttttagattttattttggaggttgagct Intra-Species Hit: Count: 1 Min: 1 Max: 105 Len: 105 Subject: NC_009009_SSA_1670_SSA_1671|Transcriptional regulator, TetR/AcrR family, putative:hypothetical protein|NEGATIVE:POSITIVE|[1669339,1669443]|105 HSP 1 e-value: 3.0E-53 bit: 208.0 Len: 105 Query Start:1 Query End:105 Subject Strand: POSITIVE Subject Start: 1 Subject End: 105 attttaacacaatcttgccacttgtcaagcatttatgttatactatacaaaaaagatagtttgctaatcaaattattttttagattttattttggaggttgagct attttaacacaatcttgccacttgtcaagcatttatgttatactatacaaaaaagatagtttgctaatcaaattattttttagattttattttggaggttgagct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUAACACAAUCUUGCCACUUGUCAAGCAUUUAUGUUAUACUAUACAAAAAAGAUAGUUUGCUAAUCAAAUUAUUUUUUAGAUUUUAUUUUGGAGGUUGAGCU .........((((((..(((.......((((....))))...........(((((((((((((.....)))))))))))))...........))))))))).... (-16.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUCAACCUCCAAAAUAAAAUCUAAAAAAUAAUUUGAUUAGCAAACUAUCUUUUUUGUAUAGUAUAACAUAAAUGCUUGACAAGUGGCAAGAUUGUGUUAAAAU ......................................((((((....(((((.(((((..(((((.......)))))..)))))....)))))..))))))... (-12.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 748 60 11 151 102 NC_009009:SSA_1670|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_1669248..1669478_NEGATIVE 211 39 9 176 137 NC_009009:SSA_1462|5end_Prephenate_dehydratase,_putative_1469767..1469997_NEGATIVE 210 70 21 175 123 NC_009009:SSA_1341|5end_Carbamoyl-phosphate_synthase_large_chain,_putative_1359827..1360057_NEGATIVE 210 97 54 187 137 NC_009009:SSA_0529|5end_Ethanolamine_utilization_protein,_putative_525945..526175_POSITIVE 195 99 53 66 17 NC_009009:SSA_0868|5end_hypothetical_protein_861535..861765_NEGATIVE 194 59 18 174 127 NC_009009:SSA_1030|5end_Transcriptional_regulator,_TetR_family,_putative_1047094..1047324_POSITIVE 193 67 29 181 148 NC_009009:SSA_1718|5end_Site-specific_DNA-methyltransferase,_putative_1705811..1706041_NEGATIVE 193 65 21 171 117 NC_009009:SSA_0720|5end_hypothetical_protein_705106..705336_POSITIVE 191 100 55 145 102 NC_009009:SSA_2047|5end_hypothetical_protein_2049953..2050183_NEGATIVE 187 43 9 228 182 NC_009009:SSA_0119|5end_50S_ribosomal_protein_L5,_putative_113692..113922_POSITIVE 181 69 23 137 91 NC_009009:SSA_1414|5end_hypothetical_protein_1425412..1425642_NEGATIVE 181 50 14 81 47 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 180 35 10 226 198 NC_009009:SSA_1225|5end_Branched-chain_amino_acid_aminotransferase,_putative_1248608..1248838_NEGATIVE 179 25 9 18 3 NC_009009:SSA_1439|5end_hypothetical_protein_1444373..1444603_NEGATIVE 179 34 1 220 176 NC_009009:SSA_0778|5end_Glycogen_synthase,_putative_760566..760796_POSITIVE 177 88 53 87 47 NC_009009:SSA_2209|5end_Penicillin-binding_protein_2A,_putative_2210372..2210602_NEGATIVE 175 60 13 123 55 NC_009009:SSA_1201|5end_hypothetical_protein_1225755..1225985_POSITIVE 174 35 8 147 119 NC_009009:SSA_2243|5end_Conserved_uncharacterized_protein_2239341..2239571_NEGATIVE 174 98 55 203 154 NC_009009:SSA_1307|5end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1326270..1326500_NEGATIVE 174 39 10 188 155 NC_009009:SSA_0782|5end_Proton-translocating_ATPase,_F0_sector,_subunit_c,_putative_766579..766809_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 210 70 21 151 99 NC_009009:SSA_1342|3end_Carbamoyl-phosphate_synthase_small_chain,_putative_1359851..1360001_NEGATIVE 203 70 22 148 96 NC_009009:SSA_1861|3end_Aminopeptidase_C,_putative_1856568..1856718_NEGATIVE 193 67 29 68 35 NC_009009:SSA_1719|3end_Conserved_uncharacterized_protein_1705924..1706074_NEGATIVE 191 100 55 114 71 NC_009009:SSA_2048|3end_Serine_acetyltransferase,_putative_2049984..2050134_NEGATIVE 191 69 28 76 37 NC_009009:SSA_0946|3end_Phosphate_transport_system_regulatory_protein,_putative_954126..954276_POSITIVE 181 69 23 135 89 NC_009009:SSA_1415|3end_Oxidoreductase,_putative_1425414..1425564_NEGATIVE 181 50 14 88 54 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 180 35 10 51 23 NC_009009:SSA_1226|3end_ParC,_putative_1248783..1248933_NEGATIVE 174 64 21 70 32 NC_009009:SSA_2329|3end_hypothetical_protein_2333169..2333319_POSITIVE 173 79 36 89 51 NC_009009:SSA_0923|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933698..933848_POSITIVE 173 99 56 64 11 NC_009009:SSA_0279|3end_Sugar-binding_transcriptional_repressor_(DeoR),_putative_273370..273520_POSITIVE 172 100 52 74 25 NC_009009:SSA_1486|3end_hypothetical_protein_1493442..1493592_POSITIVE 171 65 23 91 43 NC_009009:SSA_1586|3end_hypothetical_protein_1587730..1587880_NEGATIVE 171 30 12 137 113 NC_009009:SSA_0793|3end_DNA-entry_nuclease,_putative_775799..775949_POSITIVE 168 34 7 45 18 NC_009009:SSA_0472|3end_Precorrin-3B_C17-methyltransferase,_putative_475585..475735_POSITIVE 167 57 18 91 59 NC_009009:SSA_1749|3end_Pyruvate_formate-lyase-activating_enzyme,_putative_1734617..1734767_NEGATIVE 165 38 11 38 5 NC_009009:SSA_2045|3end_Reductase,_putative_2048427..2048577_NEGATIVE 161 36 11 150 127 NC_009009:SSA_1016|3end_Phosphoenolpyruvate_synthase,_putative_1022165..1022315_POSITIVE 161 100 51 75 29 NC_009009:SSA_0167|3end_Hypothetical_protein_(Asparagine/proline-rich)_166335..166485_POSITIVE 160 31 1 131 98 NC_009009:SSA_1451|3end_Exonuclease_RexA,_putative_1452744..1452894_NEGATIVE