Origin IGS: gggatcctcctagttttactcaaaattgaatacgatgagtcattttttgcgatactcccattttatcataaataagcaagaaattcacggataatctttcaaaactaaaaagaacttgacgctaaaatcaagttctg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cagaacttgattttagcgtcaagttctttttagttttgaaagattatccgtgaatttcttgcttatttatgataaaatgggagtatcgcaaaaaatgactcatcgtattcaattttgagtaaaactaggaggatccc Mask Tandem Repeat Region ================================================ gggatcctcctagttttactcaaaattgaatacgatgagtcattttttgcgatactcccattttatcataaataagcaagaaattcacggataatctttcaaaactaaaaagaacttgacgctaaaatcaagttctg Find is-nt database================================================ Query_seq: SMT_594:SMT_595|SMT_594:SMT_595:lysyl-tRNA synthetase:phosphoglycerate mutase:<-<-:511929..512065 137 gggatcctcctagttttactcaaaattgaatacgatgagtcattttttgcgatactcccattttatcataaataagcaagaaattcacggataatctttcaaaactaaaaagaacttgacgctaaaatcaagttctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_594:SMT_595|SMT_594:SMT_595:lysyl-tRNA synthetase:phosphoglycerate mutase:<-<-:511929..512065 137 gggatcctcctagttttactcaaaattgaatacgatgagtcattttttgcgatactcccattttatcataaataagcaagaaattcacggataatctttcaaaactaaaaagaacttgacgctaaaatcaagttctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_594:SMT_595|SMT_594:SMT_595:lysyl-tRNA synthetase:phosphoglycerate mutase:<-<-:511929..512065 137 gggatcctcctagttttactcaaaattgaatacgatgagtcattttttgcgatactcccattttatcataaataagcaagaaattcacggataatctttcaaaactaaaaagaacttgacgctaaaatcaagttctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gggatcctcctagttttactcaaaattgaatacgatgagtcattttttgcgatactcccattttatcataaataagcaagaaattcacggataatctttcaaaactaaaaagaacttgacgctaaaatcaagttctg Predict ORF larger than 30AA ================================================ gggatcctcctagttttactcaaaattgaatacgatgagtcattttttgcgatactcccattttatcataaataagcaagaaattcacggataatctttcaaaactaaaaagaacttgacgctaaaatcaagttctg 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================================================ gggatcctcctagttttactcaaaattgaatacgatgagtcattttttgcgatactcccattttatcataaataagcaagaaattcacggataatctttcaaaactaaaaagaacttgacgctaaaatcaagttctg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_594:SMT_595|SMT_594:SMT_595:lysyl-tRNA synthetase:phosphoglycerate mutase:<-<-:511929..512065 137 gggatcctcctagttttactcaaaattgaatacgatgagtcattttttgcgatactcccattttatcataaataagcaagaaattcacggataatctttcaaaactaaaaagaacttgacgctaaaatcaagttctg Intra-Species Hit: Count: 1 Min: 1 Max: 137 Len: 137 Subject: smit_SMT_594_SMT_595|lysyl-tRNA synthetase:phosphoglycerate mutase|NEGATIVE:NEGATIVE|[511929,512065]|137 HSP 1 e-value: 3.0E-72 bit: 272.0 Len: 137 Query Start:1 Query End:137 Subject Strand: POSITIVE Subject Start: 1 Subject End: 137 gggatcctcctagttttactcaaaattgaatacgatgagtcattttttgcgatactcccattttatcataaataagcaagaaattcacggataatctttcaaaactaaaaagaacttgacgctaaaatcaagttctg gggatcctcctagttttactcaaaattgaatacgatgagtcattttttgcgatactcccattttatcataaataagcaagaaattcacggataatctttcaaaactaaaaagaacttgacgctaaaatcaagttctg Inter-species Hit: Count: 3 Min: 1 Max: 130 Len: 130 Subject: NC_008533_SPD_0619_SPD_0620|hypothetical protein:lysyl-tRNA synthetase|POSITIVE:POSITIVE|[640254,640380]|127 HSP 1 e-value: 2.0E-61 bit: 236.0 Len: 127 Query Start:1 Query End:127 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 127 gggatcctcctagttttactcaaaattgaatacgatgagtcattttttgcgatactcccattttatcataaataagcaagaaattcacggataatctttcaaaactaaaaagaacttgacgctaaaa.......... gggatcctcctagttttactcaaaattgaatacgatgagtcattttttgcgatactcccattttatcataaataagcaagaaattcacggataatctttaaaaactaaaaagaacctgacgctaaaa.......... Subject: NC_003098_spr0625_spr0626|lactate oxidase, truncation:lysyl-tRNA synthetase|POSITIVE:POSITIVE|[632723,632849]|127 HSP 1 e-value: 2.0E-61 bit: 236.0 Len: 127 Query Start:1 Query End:127 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 127 gggatcctcctagttttactcaaaattgaatacgatgagtcattttttgcgatactcccattttatcataaataagcaagaaattcacggataatctttcaaaactaaaaagaacttgacgctaaaa.......... gggatcctcctagttttactcaaaattgaatacgatgagtcattttttgcgatactcccattttatcataaataagcaagaaattcacggataatctttaaaaactaaaaagaacctgacgctaaaa.......... Subject: NC_003028_SP_0711_SP_0713|amino acid ABC transporter, permease protein:lysyl-tRNA synthetase|NEGATIVE:POSITIVE|[676062,676623]|562 HSP 1 e-value: 6.0E-61 bit: 234.0 Len: 130 Query Start:1 Query End:130 Subject Strand: NEGATIVE Subject Start: 418 Subject End: 547 gggatcctcctagttttactcaaaattgaatacgatgagtcattttttgcgatactcccattttatcataaataagcaagaaattcacggataatctttcaaaactaaaaagaacttgacgctaaaatca....... gggatcctcctagttttactcaaaattgaatacgatgagtcattttttgcgacactcccattttatcataaataagcaagaaattcacggataatctttaaaaactaaaaagaacctgacgctaaaatca....... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGAUCCUCCUAGUUUUACUCAAAAUUGAAUACGAUGAGUCAUUUUUUGCGAUACUCCCAUUUUAUCAUAAAUAAGCAAGAAAUUCACGGAUAAUCUUUCAAAACUAAAAAGAACUUGACGCUAAAAUCA (((((..(((.......(((((...(((....)))))))).(((((((((.........................)))))))))....)))..)))))................................ (-14.61) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUUUAGCGUCAAGUUCUUUUUAGUUUUGAAAGAUUAUCCGUGAAUUUCUUGCUUAUUUAUGAUAAAAUGGGAGUAUCGCAAAAAAUGACUCAUCGUAUUCAAUUUUGAGUAAAACUAGGAGGAUCCC ((((......))))...((((((((((((((.((((((....((((((((((...(((((...)))))...)))))).)))).....((((....))))....))))))...)))))))))))))).... (-25.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 815 50 1 141 92 smit:SMT_594|5end_lysyl-tRNA_synthetase_511838..512068_NEGATIVE 322 86 41 148 101 smit:SMT_2125|5end_3-phosphoshikimate_1-carboxyvinyltransferase_2008872..2009102_POSITIVE 322 86 41 148 101 smit:SMT_750|5end_3-phosphoshikimate_1-carboxyvinyltransferase_655247..655477_NEGATIVE 281 70 29 134 87 smit:SMT_572|5end_fructose_repressor_490239..490469_POSITIVE 251 70 28 119 72 smit:SMT_628|5end_glucose-1-phosphate_adenylyltransferase,_GlgD_subunit_532831..533061_POSITIVE 239 67 32 111 80 smit:SMT_2029|5end_acetyltransferase,_GNAT_family_1943749..1943979_POSITIVE 239 67 32 111 80 smit:SMT_1755|5end_acetyltransferase,_GNAT_family_1733042..1733272_POSITIVE 235 52 26 230 203 smit:SMT_1345|5end_K06198_competence_protein_CoiA_1323770..1324000_NEGATIVE 223 68 38 135 104 smit:SMT_1832|5end_tagatose-6-phosphate_kinase_1800438..1800668_POSITIVE 219 65 38 111 86 smit:SMT_658|5end_hypothetical_protein_569645..569875_NEGATIVE 218 59 26 43 4 smit:SMT_745|5end_glycosyl_transferase,_group_1_family_protein_650387..650617_NEGATIVE 213 72 31 75 13 smit:SMT_342|5end_chaperone_protein_DnaJ_281800..282030_POSITIVE 211 87 41 170 115 smit:SMT_991|5end_hypothetical_protein_934425..934655_NEGATIVE 211 77 34 199 155 smit:SMT_929|5end_hypothetical_protein_883342..883572_NEGATIVE 211 128 84 64 23 smit:SMT_659|5end_hypothetical_protein_570545..570775_NEGATIVE 208 50 7 145 95 smit:SMT_1526|5end_K07720_two-component_system,_response_regulator_YesN_1510554..1510784_NEGATIVE 206 90 41 68 16 smit:SMT_1401|5end_pyruvate_dehydrogenase_E1_component_beta_subunit_1377013..1377243_POSITIVE 206 57 25 51 19 smit:SMT_1057|5end_replicative_DNA_helicase_995316..995546_POSITIVE 205 68 30 151 118 smit:SMT_1644|5end_3-isopropylmalate_dehydrogenase_1630704..1630934_POSITIVE 203 100 56 200 146 smit:SMT_336|5end_hypothetical_protein_275222..275452_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 322 86 41 56 9 smit:SMT_2124|3end_hypothetical_protein_2008860..2009010_POSITIVE 322 86 41 56 9 smit:SMT_751|3end_hypothetical_protein_655339..655489_NEGATIVE 251 70 28 129 82 smit:SMT_627|3end_glucose-1-phosphate_adenylyltransferase_532921..533071_POSITIVE 224 42 1 137 98 smit:SMT_1080|3end_CAAX_amino_terminal_protease_family_protein_1017783..1017933_NEGATIVE 223 68 38 124 93 smit:SMT_1831|3end_galactose-6-phosphate_isomerase_1800507..1800657_POSITIVE 220 69 30 65 5 smit:SMT_1662|3end_histidine_protein_kinase_1651305..1651455_NEGATIVE 218 59 26 53 14 smit:SMT_746|3end_LPS_biosynthesis_protein_650377..650527_NEGATIVE 211 87 41 66 11 smit:SMT_992|3end_hypothetical_protein_934529..934679_NEGATIVE 211 128 84 71 30 smit:SMT_660|3end_two-component_sensor_histidine_kinase_570538..570688_NEGATIVE 208 50 7 133 83 smit:SMT_1527|3end_two-component_sensor_kinase_1510566..1510716_NEGATIVE 206 57 25 50 18 smit:SMT_1056|3end_K07738_ATP-cone_domain_protein_995395..995545_POSITIVE 205 68 30 139 106 smit:SMT_1643|3end_2-isopropylmalate_synthase_1630772..1630922_POSITIVE 203 100 56 77 23 smit:SMT_335|3end_glutamine_synthetase_275179..275329_POSITIVE 202 89 42 138 78 smit:SMT_1949|3end_IS1381_transposase_protein_B_1883987..1884137_POSITIVE 200 53 11 150 97 smit:SMT_726|3end_ImpB/MucB/SamB_family_protein_630412..630562_NEGATIVE 198 68 34 145 108 smit:SMT_930|3end_ATP-dependent_RNA_helicase_883389..883539_NEGATIVE 197 53 27 147 120 smit:SMT_1794|3end_SOS_responce_UmuC_protein_1768442..1768592_NEGATIVE 192 50 5 136 86 smit:SMT_1603|3end_K05832_putative_ABC_transport_system_permease_protein_1594347..1594497_POSITIVE 191 86 42 66 18 smit:SMT_1736|3end_acetyltransferase,_GNAT_family_1719862..1720012_POSITIVE 190 50 2 62 13 smit:SMT_1750|3end_anthranilate_phosphoribosyltransferase_1729095..1729245_POSITIVE