Origin IGS: ttcttttcctaatttctaattttaatttaattttttatgtggtgctgatagattcagcgatttaatttcttactcaagatagactcaatccatgtcaaaacactttaggaaagacagtttcagactatctaacacctagccttctactattct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agaatagtagaaggctaggtgttagatagtctgaaactgtctttcctaaagtgttttgacatggattgagtctatcttgagtaagaaattaaatcgctgaatctatcagcaccacataaaaaattaaattaaaattagaaattaggaaaagaa Mask Tandem Repeat Region ================================================ ttcttttcctaatttctaattttaatttaattttttatgtggtgctgatagattcagcgatttaatttcttactcaagatagactcaatccatgtcaaaacactttaggaaagacagtttcagactatctaacacctagccttctactattct Find is-nt database================================================ Query_seq: SMT_650:SMT_651|SMT_650:SMT_651:pullulanase:DNA ligase:<-<-:559923..560075 153 ttcttttcctaatttctaattttaatttaattttttatgtggtgctgatagattcagcgatttaatttcttactcaagatagactcaatccatgtcaaaacactttaggaaagacagtttcagactatctaacacctagccttctactattct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_650:SMT_651|SMT_650:SMT_651:pullulanase:DNA ligase:<-<-:559923..560075 153 ttcttttcctaatttctaattttaatttaattttttatgtggtgctgatagattcagcgatttaatttcttactcaagatagactcaatccatgtcaaaacactttaggaaagacagtttcagactatctaacacctagccttctactattct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_650:SMT_651|SMT_650:SMT_651:pullulanase:DNA ligase:<-<-:559923..560075 153 ttcttttcctaatttctaattttaatttaattttttatgtggtgctgatagattcagcgatttaatttcttactcaagatagactcaatccatgtcaaaacactttaggaaagacagtttcagactatctaacacctagccttctactattct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcttttcctaatttctaattttaatttaattttttatgtggtgctgatagattcagcgatttaatttcttactcaagatagactcaatccatgtcaaaacactttaggaaagacagtttcagactatctaacacctagccttctactattct Predict ORF larger than 30AA ================================================ ttcttttcctaatttctaattttaatttaattttttatgtggtgctgatagattcagcgatttaatttcttactcaagatagactcaatccatgtcaaaacactttaggaaagacagtttcagactatctaacacctagccttctactattct 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================================================ ttcttttcctaatttctaattttaatttaattttttatgtggtgctgatagattcagcgatttaatttcttactcaagatagactcaatccatgtcaaaacactttaggaaagacagtttcagactatctaacacctagccttctactattct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_650:SMT_651|SMT_650:SMT_651:pullulanase:DNA ligase:<-<-:559923..560075 153 ttcttttcctaatttctaattttaatttaattttttatgtggtgctgatagattcagcgatttaatttcttactcaagatagactcaatccatgtcaaaacactttaggaaagacagtttcagactatctaacacctagccttctactattct Intra-Species Hit: Count: 1 Min: 37 Max: 153 Len: 117 Subject: smit_SMT_650_SMT_651|pullulanase:DNA ligase|NEGATIVE:NEGATIVE|[559923,560075]|153 HSP 1 e-value: 3.0E-60 bit: 232.0 Len: 117 Query Start:37 Query End:153 Subject Strand: POSITIVE Subject Start: 37 Subject End: 153 ....................................atgtggtgctgatagattcagcgatttaatttcttactcaagatagactcaatccatgtcaaaacactttaggaaagacagtttcagactatctaacacctagccttctactattct ....................................atgtggtgctgatagattcagcgatttaatttcttactcaagatagactcaatccatgtcaaaacactttaggaaagacagtttcagactatctaacacctagccttctactattct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGUGGUGCUGAUAGAUUCAGCGAUUUAAUUUCUUACUCAAGAUAGACUCAAUCCAUGUCAAAACACUUUAGGAAAGACAGUUUCAGACUAUCUAACACCUAGCCUUCUACUAUUCU ..((((.(((((.....)))))..................((((((.((.((....((((....(......)....))))..)).)).)))))).............))))...... (-18.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAUAGUAGAAGGCUAGGUGUUAGAUAGUCUGAAACUGUCUUUCCUAAAGUGUUUUGACAUGGAUUGAGUCUAUCUUGAGUAAGAAAUUAAAUCGCUGAAUCUAUCAGCACCACAU .......(((((.((((((....(((((((.....)))))))..)))..))).)))))...(((.(..((.....))..)...............(((((.....))))).)))... (-24.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 839 50 1 177 128 smit:SMT_650|5end_pullulanase_559832..560062_NEGATIVE 299 100 53 56 6 smit:SMT_1526|5end_K07720_two-component_system,_response_regulator_YesN_1510554..1510784_NEGATIVE 289 110 67 105 55 smit:SMT_893|5end_leucine_rich_protein_841311..841541_NEGATIVE 277 50 5 228 184 smit:SMT_261|5end_ImpB/MucB/SamB_family_protein_200160..200390_POSITIVE 253 39 1 100 61 smit:SMT_881|5end_peptidoglycan_branched_peptide_synthesis_protein,_alanine_adding_enzyme_829528..829758_NEGATIVE 239 45 4 64 19 smit:SMT_932|5end_tellurite_resistance_protein_885065..885295_POSITIVE 234 109 67 222 178 smit:SMT_1474|5end_K02003_1455170..1455400_POSITIVE 233 108 80 106 78 smit:SMT_446|5end_ABC-type_cobalt_transport_system,_ATPase_component_384870..385100_POSITIVE 231 78 31 151 95 smit:SMT_481|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_418240..418470_NEGATIVE 231 78 31 151 95 smit:SMT_480|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_417433..417663_NEGATIVE 231 78 31 151 95 smit:SMT_475|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_412997..413227_NEGATIVE 231 78 31 151 95 smit:SMT_474|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_411894..412124_NEGATIVE 231 78 31 151 95 smit:SMT_473|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_410614..410844_NEGATIVE 231 78 31 151 95 smit:SMT_471|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_408351..408581_NEGATIVE 230 25 2 25 1 smit:SMT_1889|5end_hypothetical_protein_1842935..1843165_POSITIVE 229 109 79 57 20 smit:SMT_2126|5end_indole-3-glycerol_phosphate_synthase_2009107..2009337_POSITIVE 229 109 79 57 20 smit:SMT_1751|5end_indole-3-glycerol_phosphate_synthase_1729012..1729242_POSITIVE 229 108 68 38 2 smit:SMT_1644|5end_3-isopropylmalate_dehydrogenase_1630704..1630934_POSITIVE 225 94 53 93 45 smit:SMT_1677|5end_transcription-repair_coupling_factor_1662112..1662342_NEGATIVE 222 22 3 142 116 smit:SMT_1537|5end_hypothetical_protein_1522668..1522898_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 289 110 67 101 51 smit:SMT_894|3end_hypothetical_protein_841315..841465_NEGATIVE 264 110 64 55 13 smit:SMT_1348|3end_exoribonuclease_II_1325148..1325298_NEGATIVE 250 42 3 62 26 smit:SMT_1998|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1922640..1922790_POSITIVE 234 109 67 91 47 smit:SMT_1473|3end_hypothetical_protein_1455119..1455269_POSITIVE 233 108 80 105 77 smit:SMT_445|3end_hypothetical_protein_384949..385099_POSITIVE 232 43 3 151 105 smit:SMT_410|3end_glucokinase_355477..355627_POSITIVE 229 60 22 43 3 smit:SMT_1862|3end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1825460..1825610_POSITIVE 229 109 79 60 23 smit:SMT_1750|3end_anthranilate_phosphoribosyltransferase_1729095..1729245_POSITIVE 227 101 67 151 108 smit:SMT_1792|3end_K03307_solute:Na+_symporter,_SSS_family_1766575..1766725_NEGATIVE 222 22 3 141 115 smit:SMT_1538|3end_two-component_response_regulator_YvqC_1522669..1522819_NEGATIVE 219 89 48 42 3 smit:SMT_2141|3end_hypothetical_protein_2018960..2019110_NEGATIVE 215 110 67 93 39 smit:SMT_199|3end_K07166_ACT_domain-containing_protein_129817..129967_POSITIVE 214 90 41 81 32 smit:SMT_2135|3end_dipeptidase_2014754..2014904_NEGATIVE 214 90 41 81 32 smit:SMT_874|3end_dipeptidase_821365..821515_NEGATIVE 213 100 65 44 3 smit:SMT_1527|3end_two-component_sensor_kinase_1510566..1510716_NEGATIVE 213 90 42 91 42 smit:SMT_1483|3end_GTP-binding_protein_1463140..1463290_NEGATIVE 206 104 63 52 9 smit:SMT_541|3end_K03697_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpE_457120..457270_NEGATIVE 205 109 66 85 28 smit:SMT_1014|3end_galactokinase_950645..950795_NEGATIVE 201 59 11 103 43 smit:SMT_1496|3end_conserved_hypothetical_protein_TIGR00150_1481522..1481672_POSITIVE 201 27 5 119 94 smit:SMT_344|3end_K02503_Hit-like_protein_involved_in_cell-cycle_regulation_283564..283714_NEGATIVE