Origin IGS: atagggaaatttccaaacggctccaagtccgatagctgaaccagcagatgctagaataaagcctagtttagaaccccattgcgatttcagacactttccagcannnnn .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 nnnnntgctggaaagtgtctgaaatcgcaatggggttctaaactaggctttattctagcatctgctggttcagctatcggacttggagccgtttggaaatttccctat Mask Tandem Repeat Region ================================================ atagggaaatttccaaacggctccaagtccgatagctgaaccagcagatgctagaataaagcctagtttagaaccccattgcgatttcagacactttccagcannnnn Find is-nt database================================================ Query_seq: SMT_479:SMT_480|SMT_479:SMT_480:K03308 neurotransmitter:Na+ symporter, NSS family:K03308 neurotransmitter:Na+ symporter, NSS family:<-<-:416747..416854 108 atagggaaatttccaaacggctccaagtccgatagctgaaccagcagatgctagaataaagcctagtttagaaccccattgcgatttcagacactttccagcannnnn Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_479:SMT_480|SMT_479:SMT_480:K03308 neurotransmitter:Na+ symporter, NSS family:K03308 neurotransmitter:Na+ symporter, NSS family:<-<-:416747..416854 108 atagggaaatttccaaacggctccaagtccgatagctgaaccagcagatgctagaataaagcctagtttagaaccccattgcgatttcagacactttccagcannnnn Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_479:SMT_480|SMT_479:SMT_480:K03308 neurotransmitter:Na+ symporter, NSS family:K03308 neurotransmitter:Na+ symporter, NSS family:<-<-:416747..416854 108 atagggaaatttccaaacggctccaagtccgatagctgaaccagcagatgctagaataaagcctagtttagaaccccattgcgatttcagacactttccagcannnnn Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atagggaaatttccaaacggctccaagtccgatagctgaaccagcagatgctagaataaagcctagtttagaaccccattgcgatttcagacactttccagcannnnn Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 1 End: 90 Y P F K W V A G L G I A S G A S A L I F G L K S G W Q S K M .................. atagggaaatttccaaacggctccaagtccgatagctgaaccagcagatgctagaataaagcctagtttagaaccccattgcgatttcagacactttccagcannnnn 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================================================ atagggaaatttccaaacggctccaagtccgatagctgaaccagcagatgctagaataaagcctagtttagaaccccattgcgatttcagacactttccagcannnnn Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_479:SMT_480|SMT_479:SMT_480:K03308 neurotransmitter:Na+ symporter, NSS family:K03308 neurotransmitter:Na+ symporter, NSS family:<-<-:416747..416854 108 atagggaaatttccaaacggctccaagtccgatagctgaaccagcagatgctagaataaagcctagtttagaaccccattgcgatttcagacactttccagcannnnn Intra-Species Hit: Count: 1 Min: 1 Max: 103 Len: 103 Subject: smit_SMT_479_SMT_480|K03308 neurotransmitter:Na+ symporter, NSS family:K03308 neurotransmitter:Na+ symporter, NSS family|NEGATIVE:NEGATIVE|[416747,416854]|108 HSP 1 e-value: 4.0E-52 bit: 204.0 Len: 103 Query Start:1 Query End:103 Subject Strand: POSITIVE Subject Start: 1 Subject End: 103 atagggaaatttccaaacggctccaagtccgatagctgaaccagcagatgctagaataaagcctagtttagaaccccattgcgatttcagacactttccagca..... atagggaaatttccaaacggctccaagtccgatagctgaaccagcagatgctagaataaagcctagtttagaaccccattgcgatttcagacactttccagca..... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAGGGAAAUUUCCAAACGGCUCCAAGUCCGAUAGCUGAACCAGCAGAUGCUAGAAUAAAGCCUAGUUUAGAACCCCAUUGCGAUUUCAGACACUUUCCAGCA ....(((((........((((.....).)))...((((((...((((..(((((........)))))...........))))...))))).)..))))).... (-18.72) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCUGGAAAGUGUCUGAAAUCGCAAUGGGGUUCUAAACUAGGCUUUAUUCUAGCAUCUGCUGGUUCAGCUAUCGGACUUGGAGCCGUUUGGAAAUUUCCCUAU .(((....))).............((((((((((((((..(((((((...((((....))))((((.......)))).)))))))))))))))....)))))) (-27.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 970 50 1 141 92 smit:SMT_479|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_416656..416886_NEGATIVE 970 50 1 141 92 smit:SMT_462|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_401658..401888_NEGATIVE 955 60 11 55 6 smit:SMT_470|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_407303..407533_NEGATIVE 884 70 21 65 16 smit:SMT_482|5end_hypothetical_protein_predicted_by_Glimmer/Critica_418536..418766_NEGATIVE 333 66 21 207 156 smit:SMT_1043|5end_chaperonin_GroEL_985766..985996_NEGATIVE 325 54 19 117 83 smit:SMT_229|5end_mechanosensitive_ion_channel_165623..165853_NEGATIVE 317 69 22 61 19 smit:SMT_210|5end_acetyltransferase,_GNAT_family_143380..143610_POSITIVE 314 66 24 73 34 smit:SMT_1453|5end_K07335_basic_membrane_protein_A_and_related_proteins_1437407..1437637_NEGATIVE 311 47 4 193 151 smit:SMT_1006|5end_6-pyruvoyl_tetrahydrobiopterin_synthase,_putative_946599..946829_POSITIVE 310 86 41 59 21 smit:SMT_1029|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_965632..965862_NEGATIVE 301 64 21 48 5 smit:SMT_1530|5end_K07456_DNA_mismatch_repair_protein_MutS2_1515346..1515576_NEGATIVE 299 46 1 222 168 smit:SMT_125|5end_hypothetical_protein_77664..77894_NEGATIVE 296 48 13 42 9 smit:SMT_1799|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1773416..1773646_POSITIVE 295 45 1 216 172 smit:SMT_1788|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1765029..1765259_NEGATIVE 293 50 4 216 172 smit:SMT_2051|5end_enoyl-CoA_hydratase_1960639..1960869_NEGATIVE 286 80 32 211 159 smit:SMT_2166|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2039569..2039799_POSITIVE 286 67 22 77 30 smit:SMT_749|5end_shikimate_kinase_653971..654201_NEGATIVE 285 100 51 54 3 smit:SMT_1627|5end_hypothetical_protein_1616415..1616645_NEGATIVE 284 54 18 42 1 smit:SMT_641|5end_PTS_system,_lactose-specific_IIA_component_547107..547337_NEGATIVE 283 46 3 204 165 smit:SMT_1129|5end_hypothetical_protein_1063926..1064156_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 516 34 1 151 118 smit:SMT_482|3end_hypothetical_protein_predicted_by_Glimmer/Critica_418414..418564_NEGATIVE 340 47 19 47 21 smit:SMT_2057|3end_cell_division_protein_FtsH_1966897..1967047_NEGATIVE 325 54 19 74 40 smit:SMT_230|3end_hypothetical_protein_predicted_by_Glimmer/Critica_165666..165816_NEGATIVE 317 69 22 49 7 smit:SMT_209|3end_acetyltransferase,_GNAT_family_143448..143598_POSITIVE 286 67 22 84 37 smit:SMT_750|3end_3-phosphoshikimate_1-carboxyvinyltransferase_653964..654114_NEGATIVE 286 93 74 22 1 smit:SMT_471|3end_K03308_neurotransmitter:Na+_symporter,_NSS_family_407371..407521_NEGATIVE 278 56 18 151 104 smit:SMT_1203|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1164221..1164371_NEGATIVE 269 57 18 58 18 smit:SMT_1047|3end_chaperonin,_10_kDa_987920..988070_NEGATIVE 269 57 18 58 18 smit:SMT_1045|3end_cochaperonin_GroES_987451..987601_NEGATIVE 267 68 25 137 97 smit:SMT_576|3end_transcriptional_regulator,_LysR_family_495407..495557_POSITIVE 265 100 51 131 91 smit:SMT_1633|3end_formate--tetrahydrofolate_ligase_1620990..1621140_POSITIVE 264 63 24 43 3 smit:SMT_157|3end_hypothetical_protein_103871..104021_POSITIVE 256 45 18 51 27 smit:SMT_1621|3end_K09134_hypothetical_protein_1607256..1607406_NEGATIVE 255 90 41 78 38 smit:SMT_1895|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1847402..1847552_POSITIVE 253 51 14 121 76 smit:SMT_1857|3end_hypothetical_protein_1821145..1821295_POSITIVE 247 47 16 149 112 smit:SMT_1307|3end_glycerol_uptake_facilitator_protein_1272448..1272598_POSITIVE 244 55 18 85 54 smit:SMT_1538|3end_two-component_response_regulator_YvqC_1522669..1522819_NEGATIVE 242 67 21 77 32 smit:SMT_964|3end_cadmium_resistance_transporter,_putative_909891..910041_NEGATIVE 242 57 13 73 17 smit:SMT_213|3end_leucyl-tRNA_synthetase_146167..146317_POSITIVE 242 70 21 87 31 smit:SMT_173|3end_50S_ribosomal_protein_L2_117407..117557_POSITIVE