Origin IGS: aattataccccgtttcagctaaattgaagtcttcattattatagacaaaattctttttttcttctatcgggaaatttagaaatatatgcgaatacttgaaaatttctaaatcttcatatatacttggtcgatataaattgacctgaggagtttaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttaaactcctcaggtcaatttatatcgaccaagtatatatgaagatttagaaattttcaagtattcgcatatatttctaaatttcccgatagaagaaaaaaagaattttgtctataataatgaagacttcaatttagctgaaacggggtataatt Mask Tandem Repeat Region ================================================ aattataccccgtttcagctaaattgaagtcttcattattatagacaaaattctttttttcttctatcgggaaatttagaaatatatgcgaatacttgaaaatttctaaatcttcatatatacttggtcgatataaattgacctgaggagtttaaa Find is-nt database================================================ Query_seq: TDE0685:TDE0686|TDE0685:TDE0686:oxidoreductase, short chain dehydrogenase/reductase family:phosphoribosylaminoimidazole-succinocarboxamide synthase:<-->:722711..722866 156 aattataccccgtttcagctaaattgaagtcttcattattatagacaaaattctttttttcttctatcgggaaatttagaaatatatgcgaatacttgaaaatttctaaatcttcatatatacttggtcgatataaattgacctgaggagtttaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0685:TDE0686|TDE0685:TDE0686:oxidoreductase, short chain dehydrogenase/reductase family:phosphoribosylaminoimidazole-succinocarboxamide synthase:<-->:722711..722866 156 aattataccccgtttcagctaaattgaagtcttcattattatagacaaaattctttttttcttctatcgggaaatttagaaatatatgcgaatacttgaaaatttctaaatcttcatatatacttggtcgatataaattgacctgaggagtttaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0685:TDE0686|TDE0685:TDE0686:oxidoreductase, short chain dehydrogenase/reductase family:phosphoribosylaminoimidazole-succinocarboxamide synthase:<-->:722711..722866 156 aattataccccgtttcagctaaattgaagtcttcattattatagacaaaattctttttttcttctatcgggaaatttagaaatatatgcgaatacttgaaaatttctaaatcttcatatatacttggtcgatataaattgacctgaggagtttaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattataccccgtttcagctaaattgaagtcttcattattatagacaaaattctttttttcttctatcgggaaatttagaaatatatgcgaatacttgaaaatttctaaatcttcatatatacttggtcgatataaattgacctgaggagtttaaa Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: - Start: 2 End: 121 . N Y G T E A L N F D E N N Y V F N K K E E I P F N L F I H S Y K F I E L D E Y M ................................... aattataccccgtttcagctaaattgaagtcttcattattatagacaaaattctttttttcttctatcgggaaatttagaaatatatgcgaatacttgaaaatttctaaatcttcatatatacttggtcgatataaattgacctgaggagtttaaa 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: 95 End: 124 ..............................................................................................CTTGAAAATTTCTAAATCTTCATATATACT................................ PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 38 End: 67 .....................................ATAGAAGAAAAAAAGAATTTTGTCTATAAT......................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 13 End: 42 ............TTTCAGCTAAATTGAAGTCTTCATTATTAT.................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aattataccccgtttcagctaaattgaagtcttcattattatagacaaaattctttttttcttctatcgggaaatttagaaatatatgcgaatacttgaaaatttctaaatcttcatatatacttggtcgatataaattgacctgaggagtttaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0685:TDE0686|TDE0685:TDE0686:oxidoreductase, short chain dehydrogenase/reductase family:phosphoribosylaminoimidazole-succinocarboxamide synthase:<-->:722711..722866 156 aattataccccgtttcagctaaattgaagtcttcattattatagacaaaattctttttttcttctatcgggaaatttagaaatatatgcgaatacttgaaaatttctaaatcttcatatatacttggtcgatataaattgacctgaggagtttaaa Intra-Species Hit: Count: 1 Min: 1 Max: 156 Len: 156 Subject: NC_002967_TDE0685_TDE0686|oxidoreductase, short chain dehydrogenase/reductase family:phosphoribosylaminoimidazole-succinocarboxamide synthase|NEGATIVE:POSITIVE|[722711,722866]|156 HSP 1 e-value: 5.0E-71 bit: 268.0 Len: 156 Query Start:1 Query End:156 Subject Strand: POSITIVE Subject Start: 1 Subject End: 156 aattataccccgtttcagctaaattgaagtcttcattattatagacaaaattcnnnnnnncttctatcgggaaatttagaaatatatgcgaatacttgaaaatttctaaatcttcatatatacttggtcgatataaattgacctgaggagtttaaa aattataccccgtttcagctaaattgaagtcttcattattatagacaaaattctttttttcttctatcgggaaatttagaaatatatgcgaatacttgaaaatttctaaatcttcatatatacttggtcgatataaattgacctgaggagtttaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUAUACCCCGUUUCAGCUAAAUUGAAGUCUUCAUUAUUAUAGACAAAAUUCUUUUUUUCUUCUAUCGGGAAAUUUAGAAAUAUAUGCGAAUACUUGAAAAUUUCUAAAUCUUCAUAUAUACUUGGUCGAUAUAAAUUGACCUGAGGAGUUUAAA .......................(((((.(((((......(((((..(((.......)))..)))))..(((.((((((((((.....(((....)))...)))))))))).)))..........(((((((....))))))).))))).))))). (-27.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAAACUCCUCAGGUCAAUUUAUAUCGACCAAGUAUAUAUGAAGAUUUAGAAAUUUUCAAGUAUUCGCAUAUAUUUCUAAAUUUCCCGAUAGAAGAAAAAAAGAAUUUUGUCUAUAAUAAUGAAGACUUCAAUUUAGCUGAAACGGGGUAUAAUU .(((.(((((...((((.((....)).)))).(((.....(((((.....(((((((..((((((......))))))..)))))))..(((((((...........)))))))..............))))).....))).....))))).))).. (-27.70) 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 NC_002967:TDE0685|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_722620..722850_NEGATIVE 264 38 9 74 33 NC_002967:TDE2461|5end_selenide,_water_dikinase_(selenocysteine-containing)_2488260..2488490_NEGATIVE 232 124 85 100 62 NC_002967:TDE2117|5end_hypothetical_protein_2147806..2148036_POSITIVE 227 148 103 147 101 NC_002967:TDE1599|5end_ABC_transporter,_ATP-binding/permease_protein_1650644..1650874_NEGATIVE 223 62 24 121 78 NC_002967:TDE1039|5end_riboflavin_biosynthesis_protein,_putative_1067072..1067302_POSITIVE 220 33 4 191 161 NC_002967:TDE2211|5end_hypothetical_protein_2251316..2251546_NEGATIVE 218 150 102 147 99 NC_002967:TDE2215|5end_galactoside_ABC_transporter,_permease_protein,_putative_2255135..2255365_NEGATIVE 217 70 23 207 164 NC_002967:TDE0017|5end_hypothetical_protein_22936..23166_NEGATIVE 215 37 8 190 156 NC_002967:TDE0931|5end_MATE_efflux_family_protein_955107..955337_NEGATIVE 211 145 102 178 128 NC_002967:TDE0564|5end_hypothetical_protein_596285..596515_POSITIVE 208 145 112 226 193 NC_002967:TDE0082|5end_transcriptional_regulator,_MerR_family_94251..94481_NEGATIVE 204 42 10 72 37 NC_002967:TDE1937|5end_hypothetical_protein_1953264..1953494_POSITIVE 201 149 113 40 2 NC_002967:TDE2611|5end_hypothetical_protein_2651980..2652210_POSITIVE 199 45 17 101 72 NC_002967:TDE2233|5end_iron_compound_ABC_transporter,_permease_protein,_putative_2272310..2272540_NEGATIVE 197 147 111 107 72 NC_002967:TDE2758|5end_hypothetical_protein_2813965..2814195_POSITIVE 196 69 23 102 41 NC_002967:TDE0768|5end_50S_ribosomal_protein_L4_806996..807226_POSITIVE 194 65 29 206 173 NC_002967:TDE2539|5end_hypothetical_protein_2565158..2565388_NEGATIVE 194 40 10 138 117 NC_002967:TDE2247|5end_PemK_family_protein_2286362..2286592_POSITIVE 194 72 50 56 29 NC_002967:TDE2132|5end_cobalt_ABC_transporter,_ATP-binding_protein,_putative_2163541..2163771_NEGATIVE 194 80 37 61 16 NC_002967:TDE1496|5end_chromosome_partition_protein_SmC,_putative_1540285..1540515_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 239 70 45 87 62 NC_002967:TDE2287|3end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_2324309..2324459_NEGATIVE 233 79 31 149 99 NC_002967:TDE2550|3end_hypothetical_protein_2575520..2575670_NEGATIVE 227 148 103 146 100 NC_002967:TDE1600|3end_ABC_transporter,_ATP-binding/permease_protein_1650645..1650795_NEGATIVE 223 47 1 65 17 NC_002967:TDE0950|3end_hypothetical_protein_974166..974316_NEGATIVE 218 150 102 122 74 NC_002967:TDE2216|3end_galactoside_ABC_transporter,_ATP-binding_protein_2255160..2255310_NEGATIVE 217 70 23 70 27 NC_002967:TDE0018|3end_LysM_domain_protein_23073..23223_NEGATIVE 211 144 101 122 79 NC_002967:TDE2490|3end_primosomal_protein_N'_2512703..2512853_NEGATIVE 211 145 102 122 72 NC_002967:TDE0563|3end_hypothetical_protein_596309..596459_POSITIVE 208 38 16 29 1 NC_002967:TDE2462|3end_hypothetical_protein_2488305..2488455_NEGATIVE 208 46 4 71 27 NC_002967:TDE0570|3end_hypothetical_protein_600956..601106_POSITIVE 204 42 10 82 47 NC_002967:TDE1936|3end_hypothetical_protein_1953354..1953504_POSITIVE 202 45 22 32 9 NC_002967:TDE1466|3end_oxygen-independent_coproporphyrinogen_III_oxidase,_putative_1515517..1515667_POSITIVE 199 45 17 101 72 NC_002967:TDE2234|3end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_2272310..2272460_NEGATIVE 198 99 56 94 45 NC_002967:TDE2679|3end_hypothetical_protein_2720482..2720632_POSITIVE 197 147 111 123 88 NC_002967:TDE2757|3end_nucleotidyltransferase_family_protein_2814061..2814211_POSITIVE 196 69 23 87 26 NC_002967:TDE0767|3end_ribosomal_protein_L3_807061..807211_POSITIVE 194 40 10 150 129 NC_002967:TDE2246|3end_hypothetical_protein_2286454..2286604_POSITIVE 194 72 50 68 41 NC_002967:TDE2133|3end_cobalt_transport_protein,_putative_2163529..2163679_NEGATIVE 188 80 31 124 80 NC_002967:TDE0689|3end_5-methylthioribose_kinase_726972..727122_POSITIVE 187 144 113 40 4 NC_002967:TDE2384|3end_phosphoglycerate_mutase_family_protein_2414296..2414446_POSITIVE