Origin IGS: gaagcgatcttggaagtagcgannnnnttaattaattaannnnngctggaaaggttataaaccaagcatataagaaaaaagatacccargattgtactgcaccccaaaagttagacagaaaaaatctaacttttggggtgttttatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aataaaacaccccaaaagttagattttttctgtctaacttttggggtgcagtacaatcytgggtatcttttttcttatatgcttggtttataacctttccagcnnnnnttaattaattaannnnntcgctacttccaagatcgcttc Mask Tandem Repeat Region ================================================ gaagcgatcttggaagtagcgannnnnttaattaattaannnnngctggaaaggttataaaccaagcatataagaaaaaagatacccargattgtactgcaccccaaaagttagacagaaaaaatctaacttttggggtgttttatt Find is-nt database================================================ Query_seq: SMT_541:SMT_542|SMT_541:SMT_542:K03697 ATP-dependent Clp protease ATP-binding subunit ClpE:hypothetical protein:<-->:457933..458079 147 gaagcgatcttggaagtagcgannnnnttaattaattaannnnngctggaaaggttataaaccaagcatataagaaaaaagatacccargattgtactgcaccccaaaagttagacagaaaaaatctaacttttggggtgttttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_541:SMT_542|SMT_541:SMT_542:K03697 ATP-dependent Clp protease ATP-binding subunit ClpE:hypothetical protein:<-->:457933..458079 147 gaagcgatcttggaagtagcgannnnnttaattaattaannnnngctggaaaggttataaaccaagcatataagaaaaaagatacccargattgtactgcaccccaaaagttagacagaaaaaatctaacttttggggtgttttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_541:SMT_542|SMT_541:SMT_542:K03697 ATP-dependent Clp protease ATP-binding subunit ClpE:hypothetical protein:<-->:457933..458079 147 gaagcgatcttggaagtagcgannnnnttaattaattaannnnngctggaaaggttataaaccaagcatataagaaaaaagatacccargattgtactgcaccccaaaagttagacagaaaaaatctaacttttggggtgttttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaagcgatcttggaagtagcgannnnnttaattaattaannnnngctggaaaggttataaaccaagcatataagaaaaaagatacccargattgtactgcaccccaaaagttagacagaaaaaatctaacttttggggtgttttatt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 57 End: 146 ........................................................ M N Q A Y K K K D T Q D C T A P Q K L D R K N L T F G V F Y . gaagcgatcttggaagtagcgannnnnttaattaattaannnnngctggaaaggttataaaccaagcatataagaaaaaagatacccargattgtactgcaccccaaaagttagacagaaaaaatctaacttttggggtgttttatt 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================================================ gaagcgatcttggaagtagcgannnnnttaattaattaannnnngctggaaaggttataaaccaagcatataagaaaaaagatacccargattgtactgcaccccaaaagttagacagaaaaaatctaacttttggggtgttttatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_541:SMT_542|SMT_541:SMT_542:K03697 ATP-dependent Clp protease ATP-binding subunit ClpE:hypothetical protein:<-->:457933..458079 147 gaagcgatcttggaagtagcgannnnnttaattaattaannnnngctggaaaggttataaaccaagcatataagaaaaaagatacccargattgtactgcaccccaaaagttagacagaaaaaatctaacttttggggtgttttatt Intra-Species Hit: Count: 1 Min: 1 Max: 147 Len: 147 Subject: smit_SMT_541_SMT_542|K03697 ATP-dependent Clp protease ATP-binding subunit ClpE:hypothetical protein|NEGATIVE:POSITIVE|[457933,458079]|147 HSP 1 e-value: 2.0E-59 bit: 229.0 Len: 147 Query Start:1 Query End:147 Subject Strand: POSITIVE Subject Start: 1 Subject End: 147 gaagcgatcttggaagtagcgannnnnttaattaattaannnnngctggaaaggttataaaccaagcatataagaaaaaagatacccargattgtactgcaccccaaaagttagacagaaaaaatctaacttttggggtgttttatt gaagcgatcttggaagtagcgannnnnttaattaattaannnnngctggaaaggttataaaccaagcatataagaaaaaagatacccargattgtactgcaccccaaaagttagacagaaaaaatctaacttttggggtgttttatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAGCGAUCUUGGAAGUAGCGANNNNNUUAAUUAAUUAANNNNNGCUGGAAAGGUUAUAAACCAAGCAUAUAAGAAAAAAGAUACCCARGAUUGUACUGCACCCCAAAAGUUAGACAGAAAAAAUCUAACUUUUGGGGUGUUUUAUU ...((((((.(((...((((.......((((....)))).....))))....(((.....)))......................))).))))))...(((((((((((((((((.........)))))))))))))))))...... (-39.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAAACACCCCAAAAGUUAGAUUUUUUCUGUCUAACUUUUGGGGUGCAGUACAAUCYUGGGUAUCUUUUUUCUUAUAUGCUUGGUUUAUAACCUUUCCAGCNNNNNUUAAUUAAUUAANNNNNUCGCUACUUCCAAGAUCGCUUC .......(((((((((((((((((.......))))))))))))))))).(((...(((.((((.....................(((.....))).....(((.....((((....)))).......)))...)))).))).))).. (-33.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 838 140 91 231 182 smit:SMT_541|5end_K03697_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpE_457842..458072_NEGATIVE 388 140 101 140 101 smit:SMT_734|5end_hypothetical_protein_639967..640197_POSITIVE 379 140 96 139 98 smit:SMT_570|5end_hypothetical_protein_488581..488811_POSITIVE 299 136 97 221 185 smit:SMT_1727|5end_uridine_kinase_1712483..1712713_POSITIVE 255 50 7 181 129 smit:SMT_1643|5end_2-isopropylmalate_synthase_1629130..1629360_POSITIVE 244 137 91 194 150 smit:SMT_675|5end_DNA_repair_protein_582977..583207_NEGATIVE 235 105 61 152 111 smit:SMT_216|5end_Holliday_junction_DNA_helicase_RuvB_148257..148487_POSITIVE 235 105 61 152 111 smit:SMT_212|5end_Holliday_junction_DNA_helicase_RuvB_144830..145060_POSITIVE 223 75 45 200 170 smit:SMT_1671|5end_hypothetical_protein_1659757..1659987_NEGATIVE 218 138 96 116 60 smit:SMT_1634|5end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_1621074..1621304_POSITIVE 216 140 92 189 143 smit:SMT_356|5end_hypothetical_protein_292394..292624_POSITIVE 213 107 61 87 45 smit:SMT_1856|5end_polypeptide_deformylase_1820650..1820880_POSITIVE 205 50 1 159 117 smit:SMT_464|5end_ribonuclease_Z_402867..403097_POSITIVE 204 70 45 166 146 smit:SMT_1915|5end_pyridoxine_biosynthesis_protein_1860329..1860559_POSITIVE 204 106 81 37 11 smit:SMT_456|5end_pyruvate_oxidase_394236..394466_POSITIVE 199 138 91 175 131 smit:SMT_413|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_356677..356907_POSITIVE 195 69 45 96 72 smit:SMT_149|5end_hypothetical_protein_predicted_by_Glimmer/Critica_98592..98822_POSITIVE 188 86 47 53 5 smit:SMT_144|5end_hypothetical_protein_predicted_by_Glimmer/Critica_95553..95783_POSITIVE 187 69 28 182 138 smit:SMT_2011|5end_lysyl-tRNA_synthetase_1930409..1930639_NEGATIVE 185 65 45 160 141 smit:SMT_1983|5end_glycerophosphoryl_diester_phosphodiesterase_1913691..1913921_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 456 117 75 84 39 smit:SMT_571|3end_putative_transposase,_ISSmu1_490009..490159_POSITIVE 311 119 93 87 61 smit:SMT_735|3end_putative_transposase,_ISSmu1_641395..641545_POSITIVE 304 139 96 50 4 smit:SMT_1761|3end_transcriptional_activator,_putative_1737185..1737335_POSITIVE 299 136 97 111 75 smit:SMT_1726|3end_tRNA_pseudouridine_synthase_B_1712453..1712603_POSITIVE 282 139 101 63 27 smit:SMT_1313|3end_extramembranal_protein_1278622..1278772_POSITIVE 244 137 91 151 107 smit:SMT_676|3end_DNA_helicase_II_583020..583170_NEGATIVE 223 75 45 151 121 smit:SMT_1672|3end_hypothetical_protein_1659806..1659956_NEGATIVE 214 140 125 31 16 smit:SMT_569|3end_Mn2+_and_Fe2+_transporter_of_the_NRAMP_family_488553..488703_POSITIVE 205 66 45 142 124 smit:SMT_1886|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1841198..1841348_POSITIVE 205 50 1 51 9 smit:SMT_463|3end_para-aminobenzoate_synthetase_component_I_/_4-amino-4-deoxychorismate_lyase_402839..402989_POSITIVE 204 70 45 81 61 smit:SMT_1914|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1860324..1860474_POSITIVE 195 69 45 25 1 smit:SMT_148|3end_glycoprotein_endopeptidase_98601..98751_POSITIVE 194 54 28 43 17 smit:SMT_1740|3end_choline_binding_protein_PcpA_1721674..1721824_NEGATIVE 187 69 28 131 87 smit:SMT_2012|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1930460..1930610_NEGATIVE 187 67 45 139 117 smit:SMT_1981|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1912868..1913018_POSITIVE 185 65 45 146 127 smit:SMT_1984|3end_phosphinothricin_N-acetyltransferase_1913705..1913855_NEGATIVE 180 75 45 137 106 smit:SMT_1874|3end_hypothetical_protein_1832623..1832773_NEGATIVE 180 104 90 121 106 smit:SMT_1487|3end_hypothetical_protein_1467076..1467226_POSITIVE 178 137 103 65 33 smit:SMT_548|3end_K02035_peptide/nickel_transport_system_substrate-binding_protein_467039..467189_POSITIVE 178 21 5 138 124 smit:SMT_415|3end_hypothetical_protein_359488..359638_POSITIVE