Origin IGS: atttacctctgttttatcattcattgtaaaaaatcgttctatactattttatcacaaatagcagtaaaagagagaaaaaagacttgattcaccaaatcaagtctcttgttagt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 actaacaagagacttgatttggtgaatcaagtcttttttctctcttttactgctatttgtgataaaatagtatagaacgattttttacaatgaatgataaaacagaggtaaat Mask Tandem Repeat Region ================================================ atttacctctgttttatcattcattgtaaaaaatcgttctatactattttatcacaaatagcagtaaaagagagaaaaaagacttgattcaccaaatcaagtctcttgttagt Find is-nt database================================================ Query_seq: SMT_917:SMT_918|SMT_917:SMT_918:hydroxymethylglutaryl-CoA synthase:hypothetical protein:<-<-:871267..871379 113 atttacctctgttttatcattcattgtaaaaaatcgttctatactattttatcacaaatagcagtaaaagagagaaaaaagacttgattcaccaaatcaagtctcttgttagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_917:SMT_918|SMT_917:SMT_918:hydroxymethylglutaryl-CoA synthase:hypothetical protein:<-<-:871267..871379 113 atttacctctgttttatcattcattgtaaaaaatcgttctatactattttatcacaaatagcagtaaaagagagaaaaaagacttgattcaccaaatcaagtctcttgttagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_917:SMT_918|SMT_917:SMT_918:hydroxymethylglutaryl-CoA synthase:hypothetical protein:<-<-:871267..871379 113 atttacctctgttttatcattcattgtaaaaaatcgttctatactattttatcacaaatagcagtaaaagagagaaaaaagacttgattcaccaaatcaagtctcttgttagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttacctctgttttatcattcattgtaaaaaatcgttctatactattttatcacaaatagcagtaaaagagagaaaaaagacttgattcaccaaatcaagtctcttgttagt Predict ORF larger than 30AA ================================================ atttacctctgttttatcattcattgtaaaaaatcgttctatactattttatcacaaatagcagtaaaagagagaaaaaagacttgattcaccaaatcaagtctcttgttagt 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================================================ atttacctctgttttatcattcattgtaaaaaatcgttctatactattttatcacaaatagcagtaaaagagagaaaaaagacttgattcaccaaatcaagtctcttgttagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_917:SMT_918|SMT_917:SMT_918:hydroxymethylglutaryl-CoA synthase:hypothetical protein:<-<-:871267..871379 113 atttacctctgttttatcattcattgtaaaaaatcgttctatactattttatcacaaatagcagtaaaagagagaaaaaagacttgattcaccaaatcaagtctcttgttagt Intra-Species Hit: Count: 1 Min: 1 Max: 113 Len: 113 Subject: smit_SMT_917_SMT_918|hydroxymethylglutaryl-CoA synthase:hypothetical protein|NEGATIVE:NEGATIVE|[871267,871379]|113 HSP 1 e-value: 5.0E-58 bit: 224.0 Len: 113 Query Start:1 Query End:113 Subject Strand: POSITIVE Subject Start: 1 Subject End: 113 atttacctctgttttatcattcattgtaaaaaatcgttctatactattttatcacaaatagcagtaaaagagagaaaaaagacttgattcaccaaatcaagtctcttgttagt atttacctctgttttatcattcattgtaaaaaatcgttctatactattttatcacaaatagcagtaaaagagagaaaaaagacttgattcaccaaatcaagtctcttgttagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUACCUCUGUUUUAUCAUUCAUUGUAAAAAAUCGUUCUAUACUAUUUUAUCACAAAUAGCAGUAAAAGAGAGAAAAAAGACUUGAUUCACCAAAUCAAGUCUCUUGUUAGU ......((((.((((((......((((..(((((.((.....)).)))))...))))......)))))).)))).....((((((((((.....))))))))))......... (-22.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUAACAAGAGACUUGAUUUGGUGAAUCAAGUCUUUUUUCUCUCUUUUACUGCUAUUUGUGAUAAAAUAGUAUAGAACGAUUUUUUACAAUGAAUGAUAAAACAGAGGUAAAU ......((((((((((((((...)))))))))))))).(((((.(((((.......((((((.(((((.((.....)).))))))))))).......))))).)))))..... (-25.44) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 794 110 61 201 152 smit:SMT_917|5end_hydroxymethylglutaryl-CoA_synthase_871176..871406_NEGATIVE 224 85 41 171 118 smit:SMT_1658|5end_hypothetical_protein_1648201..1648431_POSITIVE 210 87 42 159 116 smit:SMT_1641|5end_arginyl-tRNA_synthetase_1628253..1628483_NEGATIVE 209 36 1 197 161 smit:SMT_912|5end_fructokinase_863620..863850_NEGATIVE 206 90 60 231 196 smit:SMT_1297|5end_NMN_adenylytransferase_and_ribosylnicotinamide_kinase,_NadR_ortholog_1259870..1260100_POSITIVE 200 50 8 106 57 smit:SMT_1230|5end_hypothetical_protein_1191423..1191653_POSITIVE 200 76 32 158 110 smit:SMT_1069|5end_acetyl_xylan_esterase,_putative_1009330..1009560_POSITIVE 195 73 37 148 112 smit:SMT_919|5end_hypothetical_protein_872499..872729_NEGATIVE 193 108 61 58 19 smit:SMT_880|5end_beta-lactam_resistance_factor_828300..828530_NEGATIVE 192 100 58 91 42 smit:SMT_1775|5end_K07478_putative_ATPase_1751836..1752066_NEGATIVE 189 107 66 180 137 smit:SMT_1560|5end_DNA_polymerase_III_alpha_subunit_1548612..1548842_NEGATIVE 189 74 44 145 112 smit:SMT_976|5end_hypothetical_protein_925183..925413_NEGATIVE 189 60 13 129 87 smit:SMT_746|5end_LPS_biosynthesis_protein_651222..651452_NEGATIVE 188 104 83 216 191 smit:SMT_1878|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1836577..1836807_NEGATIVE 187 105 62 108 61 smit:SMT_1713|5end_K03284_metal_ion_transporter,_MIT_family_1700400..1700630_POSITIVE 186 50 3 138 96 smit:SMT_572|5end_fructose_repressor_490239..490469_POSITIVE 185 37 1 37 7 smit:SMT_1880|5end_hypothetical_protein_1836854..1837084_POSITIVE 185 105 63 144 103 smit:SMT_878|5end_excinuclease_ABC,_subunit_C_826249..826479_NEGATIVE 180 40 10 194 165 smit:SMT_1776|5end_K07707_two-component_system,_AgrA_family,_response_regulator_AgrA_1752407..1752637_NEGATIVE 178 45 8 65 33 smit:SMT_164|5end_hypothetical_membrane_spanning_protein_109095..109325_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 259 110 63 121 51 smit:SMT_1296|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1259802..1259952_POSITIVE 217 108 72 45 7 smit:SMT_1071|3end_hypothetical_protein_1010386..1010536_POSITIVE 212 100 51 55 5 smit:SMT_1739|3end_hypothetical_protein_1721633..1721783_POSITIVE 200 50 8 97 48 smit:SMT_1229|3end_hypothetical_protein_1191494..1191644_POSITIVE 195 73 37 59 23 smit:SMT_920|3end_serine/threonine_protein_kinase_872588..872738_NEGATIVE 194 108 62 67 19 smit:SMT_960|3end_putative_esterase_906126..906276_NEGATIVE 193 108 61 53 14 smit:SMT_881|3end_peptidoglycan_branched_peptide_synthesis_protein,_alanine_adding_enzyme_828305..828455_NEGATIVE 189 107 66 46 3 smit:SMT_1561|3end_putative_mucus_binding_protein_1548746..1548896_NEGATIVE 189 74 44 76 43 smit:SMT_977|3end_conserved_hypothetical_protein,_Rrf2_family_protein_925252..925402_NEGATIVE 185 105 63 105 64 smit:SMT_879|3end_hypothetical_protein_826288..826438_NEGATIVE 179 110 61 87 40 smit:SMT_1004|3end_thioredoxin_945824..945974_POSITIVE 179 106 73 113 67 smit:SMT_724|3end_hypothetical_protein_629770..629920_NEGATIVE 178 94 51 86 46 smit:SMT_1958|3end_tryptophan_synthase,_beta_subunit_1892052..1892202_POSITIVE 176 95 58 100 60 smit:SMT_702|3end_hypothetical_protein_611946..612096_NEGATIVE 174 77 51 145 119 smit:SMT_1754|3end_leader_peptidase_(prepilin_peptidase)_/_N-methyltransferase_1732363..1732513_NEGATIVE 174 90 41 62 16 smit:SMT_242|3end_PTS_system,_mannose-specific_IID_component_179163..179313_NEGATIVE 174 89 43 70 28 smit:SMT_148|3end_glycoprotein_endopeptidase_98601..98751_POSITIVE 170 43 6 43 4 smit:SMT_1358|3end_dihydroorotate_dehydrogenase_B_1336254..1336404_NEGATIVE 169 79 38 62 23 smit:SMT_1805|3end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_1781241..1781391_POSITIVE 169 79 38 62 23 smit:SMT_1634|3end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_1621438..1621588_POSITIVE