Origin IGS: tctaggtgaccatcctagcacagggggatcctctagagtcgacctgcaggcatgcaagctctgcattaatgaatcggccaacgcgcggggagaggcggtttgcgtattgggcgctcttccgcttcctcgctcactgactcgctgcgctcggtcgttcggctgcggcgagcggtatcagctcactcaaagnnnnnttaattaattaannnnntgctggaaagaaaaaggaaactgaaaatcaccatgt .........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 acatggtgattttcagtttcctttttctttccagcannnnnttaattaattaannnnnctttgagtgagctgataccgctcgccgcagccgaacgaccgagcgcagcgagtcagtgagcgaggaagcggaagagcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagagcttgcatgcctgcaggtcgactctagaggatccccctgtgctaggatggtcacctaga Mask Tandem Repeat Region ================================================ tctaggtgaccatcctagcacagggggatcctctagagtcgacctgcaggcatgcaagctctgcattaatgaatcggccaacgcgcggggagaggcggtttgcgtattgggcgctcttccgcttcctcgctcactgactcgctgcgctcggtcgttcggctgcggcgagcggtatcagctcactcaaagnnnnnttaattaattaannnnntgctggaaagaaaaaggaaactgaaaatcaccatgt Find is-nt database================================================ Query_seq: SMT_1981:SMT_1982|SMT_1981:SMT_1982:K03696 ATP-dependent Clp protease ATP-binding subunit ClpC:conserved hypothetical protein:->->:1912929..1913175 247 tctaggtgaccatcctagcacagggggatcctctagagtcgacctgcaggcatgcaagctctgcattaatgaatcggccaacgcgcggggagaggcggtttgcgtattgggcgctcttccgcttcctcgctcactgactcgctgcgctcggtcgttcggctgcggcgagcggtatcagctcactcaaagnnnnnttaattaattaannnnntgctggaaagaaaaaggaaactgaaaatcaccatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1981:SMT_1982|SMT_1981:SMT_1982:K03696 ATP-dependent Clp protease ATP-binding subunit ClpC:conserved hypothetical protein:->->:1912929..1913175 247 tctaggtgaccatcctagcacagggggatcctctagagtcgacctgcaggcatgcaagctctgcattaatgaatcggccaacgcgcggggagaggcggtttgcgtattgggcgctcttccgcttcctcgctcactgactcgctgcgctcggtcgttcggctgcggcgagcggtatcagctcactcaaagnnnnnttaattaattaannnnntgctggaaagaaaaaggaaactgaaaatcaccatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1981:SMT_1982|SMT_1981:SMT_1982:K03696 ATP-dependent Clp protease ATP-binding subunit ClpC:conserved hypothetical protein:->->:1912929..1913175 247 tctaggtgaccatcctagcacagggggatcctctagagtcgacctgcaggcatgcaagctctgcattaatgaatcggccaacgcgcggggagaggcggtttgcgtattgggcgctcttccgcttcctcgctcactgactcgctgcgctcggtcgttcggctgcggcgagcggtatcagctcactcaaagnnnnnttaattaattaannnnntgctggaaagaaaaaggaaactgaaaatcaccatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 86 Max: 199 Len: 114 Subject: UniRef90_Q6UUU1 Cluster: Hypothetical protein; n=1; Escherichia coli|Rep: Hypothetical protein - Escherichia coli HSP 1 e-value: 5.0E-6 bit: 52.4 Len: 114 Query Start:86 Query End:199 Subject Strand: null Subject Start: 26 Subject End: 63 ..................................................................................... R G E A V C V L G A L P L P R S L T R C A R S F G C G E R Y Q L T Q X X X N ................................................ ..................................................................................... R V S R I C D T G D I P L P R S L T R Y A R S F G C G E R Y R L T D G D G N ................................................ tctaggtgaccatcctagcacagggggatcctctagagtcgacctgcaggcatgcaagctctgcattaatgaatcggccaacgcgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntaattaannnnntgctggaaagaaaaaggaaactgaaaatcaccatgt Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 6 End: 134 ..... M T I L A Q G D P L E S T C R H A S S A L M N R P T R G E R R F A Y W A L F R F L A H ................................................................................................................. Protein_Len: 41 Strand: + Start: 73 End: 195 ........................................................................ M G Q R A G R G G L R I G R S S A S S L T D S L R S V V R L R R A V S A H S K X X .................................................... Protein_Len: 52 Strand: + Start: 44 End: 199 ........................................... M Q A C K L C I N E S A N A R G E A V C V L G A L P L P R S L T R C A R S F G C G E R Y Q L T Q X X X N ................................................ tctaggtgaccatcctagcacagggggatcctctagagtcgacctgcaggcatgcaagctctgcattaatgaatcggccaacgcgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntaattaannnnntgctggaaagaaaaaggaaactgaaaatcaccatgt 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================================================ tctaggtgaccatcctagcacagggggatcctctagagtcgacctgcaggcatgcaagctctgcattaatgaatcggccaacgcgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntaattaannnnntgctggaaagaaaaaggaaactgaaaatcaccatgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1981:SMT_1982|SMT_1981:SMT_1982:K03696 ATP-dependent Clp protease ATP-binding subunit ClpC:conserved hypothetical protein:->->:1912929..1913175 247 tctaggtgaccatcctagcacagggggatcctctagagtcgacctgcaggcatgcaagctctgcattaatgaatcggccaacgcgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntaattaannnnntgctggaaagaaaaaggaaactgaaaatcaccatgt Intra-Species Hit: Count: 1 Min: 1 Max: 247 Len: 247 Subject: smit_SMT_1981_SMT_1982|K03696 ATP-dependent Clp protease ATP-binding subunit ClpC:conserved hypothetical protein|POSITIVE:POSITIVE|[1912929,1913175]|247 HSP 1 e-value: 2.0E-40 bit: 167.0 Len: 84 Query Start:1 Query End:84 Subject Strand: POSITIVE Subject Start: 1 Subject End: 84 tctaggtgaccatcctagcacagggggatcctctagagtcgacctgcaggcatgcaagctctgcattaatgaatcggccaacgc................................................................................................................................................................... tctaggtgaccatcctagcacagggggatcctctagagtcgacctgcaggcatgcaagctctgcattaatgaatcggccaacgc................................................................................................................................................................... HSP 2 e-value: 1.0E-11 bit: 71.9 Len: 36 Query Start:212 Query End:247 Subject Strand: POSITIVE Subject Start: 212 Subject End: 247 ...................................................................................................................................................................................................................tgctggaaagaaaaaggaaactgaaaatcaccatgt ...................................................................................................................................................................................................................tgctggaaagaaaaaggaaactgaaaatcaccatgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUAGGUGACCAUCCUAGCACAGGGGGAUCCUCUAGAGUCGACCUGCAGGCAUGCAAGCUCUGCAUUAAUGAAUCGGCCAACGCGCGGGGAGAGGCGGUUUGCGUAUUGGGCGCUCUUCCGCUUCCUCGCUCACUGACUCGCUGCGCUCGGUCGUUCGGCUGCGGCGAGCGGUAUCAGCUCACUCAAAGNNNNNUUAAUUAAUUAANNNNNUGCUGGAAAGAAAAAGGAAACUGAAAAUCACCAUGU ....(((((...(((.((((.(((((...))))).((((.((.(((..((((((((.....)))))..........))).....(((((((..(((((...((((.....))))....))))))))))))..((((.((((((((((.(((....))))).))))))))))))..))).))))))..........................))))))).......((....)).....))))).... (-85.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAUGGUGAUUUUCAGUUUCCUUUUUCUUUCCAGCANNNNNUUAAUUAAUUAANNNNNCUUUGAGUGAGCUGAUACCGCUCGCCGCAGCCGAACGACCGAGCGCAGCGAGUCAGUGAGCGAGGAAGCGGAAGAGCGCCCAAUACGCAAACCGCCUCUCCCCGCGCGUUGGCCGAUUCAUUAAUGCAGAGCUUGCAUGCCUGCAGGUCGACUCUAGAGGAUCCCCCUGUGCUAGGAUGGUCACCUAGA (((.((.(((((((.((((((((.(((....((((......((((...............))))....)))).....((((((.((.((((......)).)))).))))))....))).))))))))...((((((.((.....((.((((((........))).))).))...........(((((.((......))))))))).)).)))).))))))).)).))).(((((.......))))). (-73.16) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1200 130 81 140 91 smit:SMT_2005|5end_pullulanase,_type_I_1926289..1926519_NEGATIVE 1200 130 81 208 159 smit:SMT_304|5end_hypothetical_protein_246580..246810_POSITIVE 1166 120 71 224 175 smit:SMT_1967|5end_dicarboxylate/amino_acid:cation_(Na+_or_H+)_symporter_(DAACS)_family_protein_1899683..1899913_NEGATIVE 1166 120 71 224 175 smit:SMT_1690|5end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1674779..1675009_NEGATIVE 1166 120 71 224 175 smit:SMT_779|5end_ribonuclease_BN,_putative_688530..688760_NEGATIVE 1109 90 41 231 182 smit:SMT_2008|5end_K07485_transposase_1928662..1928892_NEGATIVE 1109 90 41 194 145 smit:SMT_1955|5end_carbamoyl-phosphate_synthase_small_chain_1889408..1889638_NEGATIVE 1109 90 41 229 180 smit:SMT_1944|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1879494..1879724_NEGATIVE 1109 90 41 115 66 smit:SMT_464|5end_ribonuclease_Z_402867..403097_POSITIVE 1109 90 41 194 145 smit:SMT_388|5end_branched-chain_amino_acid_transport_system_II_carrier_protein_321172..321402_POSITIVE 1101 60 11 228 179 smit:SMT_2016|5end_tyrosine_recombinase_1933425..1933655_NEGATIVE 1101 60 11 219 170 smit:SMT_2001|5end_membrane_protease_protein_family_1923387..1923617_POSITIVE 1101 60 11 164 115 smit:SMT_1961|5end_K07485_transposase_1894206..1894436_POSITIVE 1101 60 11 208 159 smit:SMT_1954|5end_6-phospho-beta-glucosidase_1888548..1888778_POSITIVE 1101 60 11 213 164 smit:SMT_1155|5end_ABC-type_oligopeptide_transport_system,_periplasmic_component_1099665..1099895_NEGATIVE 1094 50 1 230 181 smit:SMT_1686|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1670175..1670405_POSITIVE 1032 48 1 231 184 smit:SMT_2044|5end_transcriptional_activator_TipA,_putative_1955885..1956115_NEGATIVE 654 32 1 215 184 smit:SMT_2006|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1926472..1926702_POSITIVE 536 120 74 144 93 smit:SMT_2052|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1961591..1961821_NEGATIVE 474 179 133 198 154 smit:SMT_1691|5end_putative_deoxyribonuclease_1674978..1675208_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1223 170 121 52 3 smit:SMT_780|3end_peptidase_family_U32_688752..688902_NEGATIVE 1109 90 41 65 16 smit:SMT_1956|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1889537..1889687_NEGATIVE 1109 90 41 60 11 smit:SMT_387|3end_hypothetical_protein_predicted_by_Glimmer/Critica_321118..321268_POSITIVE 532 206 165 43 1 smit:SMT_1968|3end_transcription-repair_coupling_factor_1899951..1900101_NEGATIVE 430 147 102 55 2 smit:SMT_1750|3end_anthranilate_phosphoribosyltransferase_1729095..1729245_POSITIVE 423 166 121 84 25 smit:SMT_1941|3end_hypothetical_protein_1877663..1877813_POSITIVE 415 130 83 53 5 smit:SMT_2044|3end_transcriptional_activator_TipA,_putative_1955274..1955424_NEGATIVE 415 130 83 53 5 smit:SMT_2016|3end_tyrosine_recombinase_1933021..1933171_NEGATIVE 415 130 83 63 15 smit:SMT_2001|3end_membrane_protease_protein_family_1923889..1924039_POSITIVE 415 130 83 53 5 smit:SMT_1957|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1890829..1890979_POSITIVE 415 130 83 53 5 smit:SMT_1886|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1841198..1841348_POSITIVE 415 130 83 53 5 smit:SMT_1658|3end_hypothetical_protein_1648937..1649087_POSITIVE 415 130 83 53 5 smit:SMT_1558|3end_hypothetical_protein_1543855..1544005_NEGATIVE 415 130 83 53 5 smit:SMT_1155|3end_ABC-type_oligopeptide_transport_system,_periplasmic_component_1099183..1099333_NEGATIVE 408 105 84 22 1 smit:SMT_463|3end_para-aminobenzoate_synthetase_component_I_/_4-amino-4-deoxychorismate_lyase_402839..402989_POSITIVE 406 170 121 53 1 smit:SMT_1946|3end_sucrose-6-phosphate_hydrolase_1881205..1881355_POSITIVE 406 69 28 111 56 smit:SMT_1786|3end_phenylalanyl-tRNA_synthetase_beta_chain_1763235..1763385_NEGATIVE 396 170 122 151 87 smit:SMT_977|3end_conserved_hypothetical_protein,_Rrf2_family_protein_925252..925402_NEGATIVE 388 130 83 53 5 smit:SMT_2006|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1926803..1926953_POSITIVE 372 180 132 70 11 smit:SMT_1630|3end_hypothetical_protein_1618141..1618291_POSITIVE