Origin IGS: gacactcttccttttacaaaattcattccattataccatttttaagaccatttgacgaccctaaaaaaatcttgggcttattttaaacaaaaaaagaggtttccccctttttc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaaaaagggggaaacctctttttttgtttaaaataagcccaagatttttttagggtcgtcaaatggtcttaaaaatggtataatggaatgaattttgtaaaaggaagagtgtc Mask Tandem Repeat Region ================================================ gacactcttccttttacaaaattcattccattataccatttttaagaccatttgacgaccctaaaaaaatcttgggcttattttaaacaaaaaaagaggtttccccctttttc Find is-nt database================================================ Query_seq: SMT_773:SMT_774|SMT_773:SMT_774:UDP-N-acetylenolpyruvoylglucosamine reductase:hypothetical protein:<-<-:684456..684568 113 gacactcttccttttacaaaattcattccattataccatttttaagaccatttgacgaccctaaaaaaatcttgggcttattttaaacaaaaaaagaggtttccccctttttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_773:SMT_774|SMT_773:SMT_774:UDP-N-acetylenolpyruvoylglucosamine reductase:hypothetical protein:<-<-:684456..684568 113 gacactcttccttttacaaaattcattccattataccatttttaagaccatttgacgaccctaaaaaaatcttgggcttattttaaacaaaaaaagaggtttccccctttttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_773:SMT_774|SMT_773:SMT_774:UDP-N-acetylenolpyruvoylglucosamine reductase:hypothetical protein:<-<-:684456..684568 113 gacactcttccttttacaaaattcattccattataccatttttaagaccatttgacgaccctaaaaaaatcttgggcttattttaaacaaaaaaagaggtttccccctttttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gacactcttccttttacaaaattcattccattataccatttttaagaccatttgacgaccctaaaaaaatcttgggcttattttaaacaaaaaaagaggtttccccctttttc Predict ORF larger than 30AA ================================================ gacactcttccttttacaaaattcattccattataccatttttaagaccatttgacgaccctaaaaaaatcttgggcttattttaaacaaaaaaagaggtttccccctttttc Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 85 Start: 30 End: 59 .............................GTCGTCAAATGGTCTTAAAAATGGTATAAT...................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gacactcttccttttacaaaattcattccattataccatttttaagaccatttgacgaccctaaaaaaatcttgggcttattttaaacaaaaaaagaggtttccccctttttc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_773:SMT_774|SMT_773:SMT_774:UDP-N-acetylenolpyruvoylglucosamine reductase:hypothetical protein:<-<-:684456..684568 113 gacactcttccttttacaaaattcattccattataccatttttaagaccatttgacgaccctaaaaaaatcttgggcttattttaaacaaaaaaagaggtttccccctttttc Intra-Species Hit: Count: 1 Min: 1 Max: 113 Len: 113 Subject: smit_SMT_773_SMT_774|UDP-N-acetylenolpyruvoylglucosamine reductase:hypothetical protein|NEGATIVE:NEGATIVE|[684456,684568]|113 HSP 1 e-value: 5.0E-33 bit: 141.0 Len: 113 Query Start:1 Query End:113 Subject Strand: POSITIVE Subject Start: 1 Subject End: 113 gacactcttccttttacaaaattcattccattataccatttttaagaccatttgacgaccctnnnnnnntcttgggcttattttaaacnnnnnnngaggtttccccctttttc gacactcttccttttacaaaattcattccattataccatttttaagaccatttgacgaccctaaaaaaatcttgggcttattttaaacaaaaaaagaggtttccccctttttc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACACUCUUCCUUUUACAAAAUUCAUUCCAUUAUACCAUUUUUAAGACCAUUUGACGACCCUAAAAAAAUCUUGGGCUUAUUUUAAACAAAAAAAGAGGUUUCCCCCUUUUUC ..........................................((((.(((......................))).))))............(((((((......))))))). ( -7.95) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAAAGGGGGAAACCUCUUUUUUUGUUUAAAAUAAGCCCAAGAUUUUUUUAGGGUCGUCAAAUGGUCUUAAAAAUGGUAUAAUGGAAUGAAUUUUGUAAAAGGAAGAGUGUC ((((((((((....))))))))))....((((((.(..(((..((.((((((((..(((...)))..))))))))....))..)))..)..))))))................ (-25.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 777 80 31 171 122 smit:SMT_773|5end_UDP-N-acetylenolpyruvoylglucosamine_reductase_684365..684595_NEGATIVE 258 39 3 131 94 smit:SMT_1737|5end_peptidyl-prolyl_cis-trans_isomerase_1719862..1720092_POSITIVE 251 110 72 175 125 smit:SMT_1217|5end_hypothetical_protein_1176603..1176833_NEGATIVE 245 108 76 144 110 smit:SMT_1667|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1657567..1657797_NEGATIVE 240 47 2 139 95 smit:SMT_1560|5end_DNA_polymerase_III_alpha_subunit_1548612..1548842_NEGATIVE 220 50 3 135 92 smit:SMT_1451|5end_K02057_simple_sugar_transport_system_permease_protein_1434683..1434913_NEGATIVE 216 62 22 201 152 smit:SMT_1098|5end_hypothetical_protein_1041992..1042222_NEGATIVE 215 110 70 228 182 smit:SMT_1304|5end_hypothetical_protein_1266630..1266860_POSITIVE 215 50 8 137 98 smit:SMT_589|5end_hypothetical_protein_505581..505811_POSITIVE 211 49 3 228 189 smit:SMT_910|5end_type_I_restriction_enzyme_R_protein_861889..862119_NEGATIVE 209 38 4 124 97 smit:SMT_1166|5end_DNA-binding_response_regulator_CiaR_1112484..1112714_NEGATIVE 209 78 34 227 175 smit:SMT_977|5end_conserved_hypothetical_protein,_Rrf2_family_protein_925689..925919_NEGATIVE 209 61 26 184 142 smit:SMT_235|5end_hypothetical_protein_174081..174311_POSITIVE 208 78 37 119 76 smit:SMT_321|5end_hypothetical_protein_259930..260160_POSITIVE 205 48 5 72 36 smit:SMT_1514|5end_methylenetetrahydrofolate_dehydrogenase_(NADP+)_/_methenyltetrahydrofolate_cyclohydrolase_1496640..1496870_NEGATIVE 203 37 6 128 92 smit:SMT_505|5end_peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type_437106..437336_NEGATIVE 203 37 6 128 92 smit:SMT_502|5end_peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type_435675..435905_NEGATIVE 203 54 25 154 118 smit:SMT_168|5end_anaerobic_ribonucleoside-triphosphate_reductase_activating_protein_113670..113900_POSITIVE 201 80 36 62 22 smit:SMT_841|5end_dihydrodipicolinate_reductase_788025..788255_NEGATIVE 200 80 47 67 38 smit:SMT_855|5end_dihydrofolate_reductase_799998..800228_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 258 39 3 51 14 smit:SMT_1736|3end_acetyltransferase,_GNAT_family_1719862..1720012_POSITIVE 251 110 72 90 40 smit:SMT_1218|3end_DNA_polymerase_I_1176688..1176838_NEGATIVE 245 108 76 88 54 smit:SMT_1668|3end_K+_transport_system,_NAD-binding_component_1657623..1657773_NEGATIVE 233 99 56 43 2 smit:SMT_517|3end_hypothetical_protein_443191..443341_POSITIVE 220 50 3 142 99 smit:SMT_1452|3end_ABC-type_uncharacterized_transport_system,_ATPase_component_1434676..1434826_NEGATIVE 218 110 72 58 19 smit:SMT_1962|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1894848..1894998_NEGATIVE 216 62 22 149 100 smit:SMT_1099|3end_protein_tyrosine_phosphatase_1042044..1042194_NEGATIVE 209 78 34 151 99 smit:SMT_978|3end_hypothetical_protein_925765..925915_NEGATIVE 209 110 76 89 53 smit:SMT_364|3end_ribosome-binding_factor_A_301353..301503_POSITIVE 203 110 71 81 32 smit:SMT_1620|3end_hypothetical_protein_1606695..1606845_NEGATIVE 198 78 42 66 28 smit:SMT_381|3end_hypothetical_protein_317437..317587_POSITIVE 198 78 42 66 28 smit:SMT_371|3end_hypothetical_protein_305906..306056_POSITIVE 196 108 90 88 69 smit:SMT_2045|3end_K+_transport_system,_NAD-binding_component_1956758..1956908_POSITIVE 195 99 53 79 20 smit:SMT_568|3end_hypothetical_protein_486389..486539_POSITIVE 189 29 6 29 6 smit:SMT_497|3end_hypothetical_protein_431810..431960_POSITIVE 186 77 34 64 14 smit:SMT_953|3end_hypothetical_protein_900899..901049_NEGATIVE 185 47 4 150 102 smit:SMT_707|3end_hypothetical_protein_predicted_by_Glimmer/Critica_616239..616389_NEGATIVE 183 77 37 49 4 smit:SMT_1748|3end_anthranilate_synthase_component_I_1727517..1727667_POSITIVE 182 74 36 80 25 smit:SMT_921|3end_putative_PP2C_protein_phosphatase_874498..874648_NEGATIVE 182 67 22 76 11 smit:SMT_571|3end_putative_transposase,_ISSmu1_490009..490159_POSITIVE