Origin IGS: agaatttcctttctatttgaggtgattattggatcacacattctattttactattatatgaaaaaatacatagaatagcaattaaacaattcgacgtaaataagtattctatttg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 caaatagaatacttatttacgtcgaattgtttaattgctattctatgtattttttcatataatagtaaaatagaatgtgtgatccaataatcacctcaaatagaaaggaaattct Mask Tandem Repeat Region ================================================ agaatttcctttctatttgaggtgattattggatcacacattctattttactattatatgaaaaaatacatagaatagcaattaaacaattcgacgtaaataagtattctatttg Find is-nt database================================================ Query_seq: SMT_1102:SMT_1103|SMT_1102:SMT_1103:transketolase:hypothetical protein:<-<-:1045096..1045210 115 agaatttcctttctatttgaggtgattattggatcacacattctattttactattatatgaaaaaatacatagaatagcaattaaacaattcgacgtaaataagtattctatttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1102:SMT_1103|SMT_1102:SMT_1103:transketolase:hypothetical protein:<-<-:1045096..1045210 115 agaatttcctttctatttgaggtgattattggatcacacattctattttactattatatgaaaaaatacatagaatagcaattaaacaattcgacgtaaataagtattctatttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1102:SMT_1103|SMT_1102:SMT_1103:transketolase:hypothetical protein:<-<-:1045096..1045210 115 agaatttcctttctatttgaggtgattattggatcacacattctattttactattatatgaaaaaatacatagaatagcaattaaacaattcgacgtaaataagtattctatttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agaatttcctttctatttgaggtgattattggatcacacattctattttactattatatgaaaaaatacatagaatagcaattaaacaattcgacgtaaataagtattctatttg Predict ORF larger than 30AA ================================================ agaatttcctttctatttgaggtgattattggatcacacattctattttactattatatgaaaaaatacatagaatagcaattaaacaattcgacgtaaataagtattctatttg 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: 88 Start: 53 End: 82 ....................................................ATTGCTATTCTATGTATTTTTTCATATAAT................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agaatttcctttctatttgaggtgattattggatcacacattctattttactattatatgaaaaaatacatagaatagcaattaaacaattcgacgtaaataagtattctatttg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1102:SMT_1103|SMT_1102:SMT_1103:transketolase:hypothetical protein:<-<-:1045096..1045210 115 agaatttcctttctatttgaggtgattattggatcacacattctattttactattatatgaaaaaatacatagaatagcaattaaacaattcgacgtaaataagtattctatttg Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: smit_SMT_1102_SMT_1103|transketolase:hypothetical protein|NEGATIVE:NEGATIVE|[1045096,1045210]|115 HSP 1 e-value: 3.0E-59 bit: 228.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 agaatttcctttctatttgaggtgattattggatcacacattctattttactattatatgaaaaaatacatagaatagcaattaaacaattcgacgtaaataagtattctatttg agaatttcctttctatttgaggtgattattggatcacacattctattttactattatatgaaaaaatacatagaatagcaattaaacaattcgacgtaaataagtattctatttg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAUUUCCUUUCUAUUUGAGGUGAUUAUUGGAUCACACAUUCUAUUUUACUAUUAUAUGAAAAAAUACAUAGAAUAGCAAUUAAACAAUUCGACGUAAAUAAGUAUUCUAUUUG (((((...(((..(((((((.((((((....)))))).............(((((.((((........)))).)))))............)))).)))...))).)))))..... (-14.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAAUAGAAUACUUAUUUACGUCGAAUUGUUUAAUUGCUAUUCUAUGUAUUUUUUCAUAUAAUAGUAAAAUAGAAUGUGUGAUCCAAUAAUCACCUCAAAUAGAAAGGAAAUUCU .((((((.....)))))).....(((((......((((((((.((((........)))).)))))))).......((.(((((......)))))..))...........))))). (-16.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 742 50 1 141 92 smit:SMT_1102|5end_transketolase_1045005..1045235_NEGATIVE 239 39 2 57 16 smit:SMT_1056|5end_K07738_ATP-cone_domain_protein_994842..995072_POSITIVE 237 107 69 84 48 smit:SMT_959|5end_1-acyl-sn-glycerol-3-phosphate_acyltransferase_905283..905513_POSITIVE 237 107 69 84 48 smit:SMT_955|5end_acyltransferase_family_protein_904096..904326_POSITIVE 218 46 1 146 97 smit:SMT_1369|5end_alanine_dehydrogenase_1348280..1348510_POSITIVE 203 48 3 59 20 smit:SMT_1741|5end_surface_protein_PspA_precursor_1723394..1723624_NEGATIVE 203 37 1 123 93 smit:SMT_1146|5end_maltose_operon_transcriptional_repressor_1090136..1090366_POSITIVE 203 50 1 160 94 smit:SMT_314|5end_biotin_carboxylase_254277..254507_POSITIVE 202 48 1 105 63 smit:SMT_1801|5end_heavy_metal_translocating_P-type_ATPase_1773916..1774146_POSITIVE 199 37 8 126 98 smit:SMT_190|5end_preprotein_translocase,_SecY_subunit_124285..124515_POSITIVE 197 48 5 212 172 smit:SMT_707|5end_hypothetical_protein_predicted_by_Glimmer/Critica_617120..617350_NEGATIVE 197 40 5 136 97 smit:SMT_169|5end_30S_ribosomal_protein_S10_114515..114745_POSITIVE 195 34 5 122 96 smit:SMT_747|5end_transcriptional_regulator,_LytR_family_652653..652883_NEGATIVE 195 44 11 220 194 smit:SMT_302|5end_K07444_putative_N6-adenine-specific_DNA_methylase_244808..245038_POSITIVE 191 32 1 150 116 smit:SMT_1099|5end_protein_tyrosine_phosphatase_1042241..1042471_NEGATIVE 186 45 1 152 93 smit:SMT_1421|5end_K02003_1407342..1407572_NEGATIVE 185 60 11 219 172 smit:SMT_896|5end_hypothetical_protein_844003..844233_NEGATIVE 184 34 1 120 93 smit:SMT_854|5end_hypothetical_protein_799492..799722_NEGATIVE 184 48 5 156 106 smit:SMT_522|5end_K02003_446719..446949_POSITIVE 182 44 1 131 93 smit:SMT_1638|5end_UTP-glucose-1-phosphate_uridylyltransferase_1624781..1625011_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 203 37 1 113 83 smit:SMT_1145|3end_maltodextrose_utilization_protein_MalA_1090206..1090356_POSITIVE 203 50 1 148 82 smit:SMT_313|3end_3R-hydroxymyristoyl_ACP_dehydrase_254345..254495_POSITIVE 199 37 8 113 85 smit:SMT_189|3end_50S_ribosomal_protein_L15_124352..124502_POSITIVE 195 34 5 125 99 smit:SMT_748|3end_prephenate_dehydratase_652650..652800_NEGATIVE 191 32 1 45 11 smit:SMT_1100|3end_putative_protein-tyrosine_phosphatase_1042346..1042496_NEGATIVE 186 45 1 137 78 smit:SMT_1422|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1407357..1407507_NEGATIVE 184 34 1 120 93 smit:SMT_855|3end_dihydrofolate_reductase_799492..799642_NEGATIVE 182 44 1 109 71 smit:SMT_1639|3end_glycerol-3-phosphate_dehydrogenase_(NAD(P)+)_1624803..1624953_NEGATIVE 178 36 1 69 37 smit:SMT_1580|3end_MutT/NUDIX_family_protein_1573153..1573303_POSITIVE 178 36 1 69 37 smit:SMT_1573|3end_MutT/NUDIX_family_protein_1566960..1567110_POSITIVE 176 45 5 137 87 smit:SMT_1414|3end_hypothetical_protein_1397361..1397511_NEGATIVE 175 39 5 131 101 smit:SMT_402|3end_two-component_response_regulator_YesN_331663..331813_POSITIVE 174 44 5 91 59 smit:SMT_1492|3end_DNA-directed_RNA_polymerase_beta_chain_1475778..1475928_POSITIVE 172 45 5 122 74 smit:SMT_179|3end_ribosomal_protein_S17_119732..119882_POSITIVE 171 24 5 102 83 smit:SMT_1461|3end_putative_phosphate_ABC_transporter_(ATP-binding_protein)_1443207..1443357_POSITIVE 170 34 1 81 43 smit:SMT_485|3end_hypothetical_protein_420229..420379_NEGATIVE 170 38 5 38 7 smit:SMT_356|3end_hypothetical_protein_293268..293418_POSITIVE 170 43 4 119 78 smit:SMT_117|3end_K02025_multiple_sugar_transport_system_permease_protein_69496..69646_POSITIVE 166 43 4 121 81 smit:SMT_1595|3end_oligopeptide_transport_system_permease_protein_OppC_1585974..1586124_POSITIVE 166 37 4 101 67 smit:SMT_231|3end_translation_elongation_factor_G_168222..168372_POSITIVE