Origin IGS: tgataaaaagaacagtttcgactgttctttttatcttctttttatgaaccaatcactactactttctatttgtcaaccatcacgctgacactataattgatttcaaacgggg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ccccgtttgaaatcaattatagtgtcagcgtgatggttgacaaatagaaagtagtagtgattggttcataaaaagaagataaaaagaacagtcgaaactgttctttttatca Mask Tandem Repeat Region ================================================ tgataaaaagaacagtttcgactgttctttttatcttctttttatgaaccaatcactactactttctatttgtcaaccatcacgctgacactataattgatttcaaacgggg Find is-nt database================================================ Query_seq: SMT_716:SMT_717|SMT_716:SMT_717:50S ribosomal protein L31:Mn2+ and Fe2+ transporter of the NRAMP family:-><-:622793..622904 112 tgataaaaagaacagtttcgactgttctttttatcttctttttatgaaccaatcactactactttctatttgtcaaccatcacgctgacactataattgatttcaaacgggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_716:SMT_717|SMT_716:SMT_717:50S ribosomal protein L31:Mn2+ and Fe2+ transporter of the NRAMP family:-><-:622793..622904 112 tgataaaaagaacagtttcgactgttctttttatcttctttttatgaaccaatcactactactttctatttgtcaaccatcacgctgacactataattgatttcaaacgggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_716:SMT_717|SMT_716:SMT_717:50S ribosomal protein L31:Mn2+ and Fe2+ transporter of the NRAMP family:-><-:622793..622904 112 tgataaaaagaacagtttcgactgttctttttatcttctttttatgaaccaatcactactactttctatttgtcaaccatcacgctgacactataattgatttcaaacgggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgataaaaagaacagtttcgactgttctttttatcttctttttatgaaccaatcactactactttctatttgtcaaccatcacgctgacactataattgatttcaaacgggg Predict ORF larger than 30AA ================================================ tgataaaaagaacagtttcgactgttctttttatcttctttttatgaaccaatcactactactttctatttgtcaaccatcacgctgacactataattgatttcaaacgggg 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================================================ tgataaaaagaacagtttcgactgttctttttatcttctttttatgaaccaatcactactactttctatttgtcaaccatcacgctgacactataattgatttcaaacgggg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_716:SMT_717|SMT_716:SMT_717:50S ribosomal protein L31:Mn2+ and Fe2+ transporter of the NRAMP family:-><-:622793..622904 112 tgataaaaagaacagtttcgactgttctttttatcttctttttatgaaccaatcactactactttctatttgtcaaccatcacgctgacactataattgatttcaaacgggg Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: smit_SMT_716_SMT_717|50S ribosomal protein L31:Mn2+ and Fe2+ transporter of the NRAMP family|POSITIVE:NEGATIVE|[622793,622904]|112 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 tgataaaaagaacagtttcgactgttctttttatcttctttttatgaaccaatcactactactttctatttgtcaaccatcacgctgacactataattgatttcaaacgggg tgataaaaagaacagtttcgactgttctttttatcttctttttatgaaccaatcactactactttctatttgtcaaccatcacgctgacactataattgatttcaaacgggg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUAAAAAGAACAGUUUCGACUGUUCUUUUUAUCUUCUUUUUAUGAACCAAUCACUACUACUUUCUAUUUGUCAACCAUCACGCUGACACUAUAAUUGAUUUCAAACGGGG .(((((((((((((((....))))))))))))))).............((....................(((((.(......).)))))......(((....)))..)).. (-24.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCCGUUUGAAAUCAAUUAUAGUGUCAGCGUGAUGGUUGACAAAUAGAAAGUAGUAGUGAUUGGUUCAUAAAAAGAAGAUAAAAAGAACAGUCGAAACUGUUCUUUUUAUCA .......((((.((((((((..(((((((......)))))))..............)))))))))))).........(((((((((((((((....))))))))))))))). (-33.29) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 261 108 62 48 8 smit:SMT_1398|5end_dihydroorotase_1373204..1373434_POSITIVE 254 88 56 164 124 smit:SMT_356|5end_hypothetical_protein_292394..292624_POSITIVE 243 80 31 221 168 smit:SMT_1683|5end_phenylalanyl-tRNA_synthetase_beta_chain_1667171..1667401_NEGATIVE 239 100 59 59 17 smit:SMT_1842|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1807858..1808088_NEGATIVE 239 100 59 147 105 smit:SMT_1841|5end_hypothetical_protein_1807770..1808000_NEGATIVE 239 94 52 163 119 smit:SMT_628|5end_glucose-1-phosphate_adenylyltransferase,_GlgD_subunit_532831..533061_POSITIVE 233 46 1 203 153 smit:SMT_1418|5end_lysine_decarboxylase_1403147..1403377_NEGATIVE 232 79 35 208 157 smit:SMT_1589|5end_hypothetical_protein_1578332..1578562_POSITIVE 231 50 1 126 70 smit:SMT_476|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_414134..414364_NEGATIVE 230 90 48 221 180 smit:SMT_690|5end_pyrimidine_regulatory_protein_602168..602398_NEGATIVE 229 70 26 142 91 smit:SMT_977|5end_conserved_hypothetical_protein,_Rrf2_family_protein_925689..925919_NEGATIVE 226 57 20 130 87 smit:SMT_784|5end_hypothetical_protein_696298..696528_NEGATIVE 218 40 6 223 185 smit:SMT_1474|5end_K02003_1455170..1455400_POSITIVE 217 50 1 114 64 smit:SMT_1993|5end_hypothetical_protein_1919800..1920030_NEGATIVE 216 110 77 42 5 smit:SMT_2066|5end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1973105..1973335_POSITIVE 216 110 77 42 5 smit:SMT_1321|5end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1290674..1290904_POSITIVE 212 85 50 166 132 smit:SMT_397|5end_NAD(+)_synthetase_326519..326749_POSITIVE 211 32 1 217 182 smit:SMT_926|5end_guanylate_kinase_880934..881164_NEGATIVE 210 103 67 45 5 smit:SMT_1042|5end_hypothetical_cytosolic_protein_984972..985202_NEGATIVE 209 69 24 84 38 smit:SMT_647|5end_DNA_gyrase,_A_subunit_554170..554400_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 348 50 2 102 56 smit:SMT_716|3end_50S_ribosomal_protein_L31_622732..622882_POSITIVE 268 79 31 107 45 smit:SMT_773|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase_683460..683610_NEGATIVE 247 44 5 98 57 smit:SMT_1170|3end_acetyltransferase,_CysE/LacA/LpxA/NodL_family_1117569..1117719_NEGATIVE 246 64 23 139 92 smit:SMT_1561|3end_putative_mucus_binding_protein_1548746..1548896_NEGATIVE 243 80 31 144 91 smit:SMT_1684|3end_acetyltransferase,_GNAT_family_1667248..1667398_NEGATIVE 239 100 59 133 91 smit:SMT_1842|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1807784..1807934_NEGATIVE 236 54 13 114 60 smit:SMT_1473|3end_hypothetical_protein_1455119..1455269_POSITIVE 229 70 26 66 15 smit:SMT_978|3end_hypothetical_protein_925765..925915_NEGATIVE 226 57 20 121 78 smit:SMT_785|3end_hypothetical_protein_696307..696457_NEGATIVE 216 110 77 42 5 smit:SMT_2065|3end_transcriptional_regulator,_MarR_family_1973185..1973335_POSITIVE 216 110 77 42 5 smit:SMT_1320|3end_transcriptional_regulator,_MarR_family_1290754..1290904_POSITIVE 211 32 1 105 70 smit:SMT_927|3end_KH_domain_protein_881046..881196_NEGATIVE 209 83 45 150 111 smit:SMT_2142|3end_hypothetical_protein_predicted_by_Glimmer/Critica_2020252..2020402_POSITIVE 203 34 2 94 61 smit:SMT_1503|3end_SSU_ribosomal_protein_S20P_1487231..1487381_POSITIVE 203 42 2 88 37 smit:SMT_936|3end_cobyric_acid_synthase_889531..889681_POSITIVE 203 42 2 88 37 smit:SMT_931|3end_cobyric_acid_synthase_885017..885167_POSITIVE 196 58 15 122 66 smit:SMT_315|3end_acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_beta_256627..256777_POSITIVE 194 47 8 110 65 smit:SMT_2029|3end_acetyltransferase,_GNAT_family_1944284..1944434_POSITIVE 194 47 8 110 65 smit:SMT_1755|3end_acetyltransferase,_GNAT_family_1733577..1733727_POSITIVE 193 82 41 100 44 smit:SMT_249|3end_hypothetical_protein_predicted_by_Glimmer/Critica_184729..184879_POSITIVE