Origin IGS: caccttttttactttgatttagcttattttttctatgtgaatctttacttgatataaaatctatcggattggcattgcaaaatatattgggttgatattcaaaaatctatcggattggcattgcaaaatatataggattggtatataatttatttactaggaattttat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ataaaattcctagtaaataaattatataccaatcctatatattttgcaatgccaatccgatagatttttgaatatcaacccaatatattttgcaatgccaatccgatagattttatatcaagtaaagattcacatagaaaaaataagctaaatcaaagtaaaaaaggtg Mask Tandem Repeat Region ================================================ caccttttttactttgatttagcttattttttctatgtgaatctttacttgatatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntatataatttatttactaggaattttat Find is-nt database================================================ Query_seq: TDE1401:TDE1402|TDE1401:TDE1402:DedA family protein:hypothetical protein:->->:1443129..1443297 169 caccttttttactttgatttagcttattttttctatgtgaatctttacttgatataaaatctatcggattggcattgcaaaatatattgggttgatattcaaaaatctatcggattggcattgcaaaatatataggattggtatataatttatttactaggaattttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1401:TDE1402|TDE1401:TDE1402:DedA family protein:hypothetical protein:->->:1443129..1443297 169 caccttttttactttgatttagcttattttttctatgtgaatctttacttgatataaaatctatcggattggcattgcaaaatatattgggttgatattcaaaaatctatcggattggcattgcaaaatatataggattggtatataatttatttactaggaattttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1401:TDE1402|TDE1401:TDE1402:DedA family protein:hypothetical protein:->->:1443129..1443297 169 caccttttttactttgatttagcttattttttctatgtgaatctttacttgatataaaatctatcggattggcattgcaaaatatattgggttgatattcaaaaatctatcggattggcattgcaaaatatataggattggtatataatttatttactaggaattttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caccttttttactttgatttagcttattttttctatgtgaatctttacttgatataaaatctatcggattggcattgcaaaatatattgggttgatattcaaaaatctatcggattggcattgcaaaatatataggattggtatataatttatttactaggaattttat Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 64 End: 153 ............................................................... R I P M A F Y I P N I N L F R D S Q C Q L I Y L I P I Y N M ................ Protein_Len: 35 Strand: - Start: 2 End: 106 . G K K S Q N L K N K R H S D K S S I F D I P N A N C F I N P Q Y E F M ............................................................... caccttttttactttgatttagcttattttttctatgtgaatctttacttgatataaaatctatcggattggcattgcaaaatatattgggttgatattcaaaaatctatcggattggcattgcaaaatatataggattggtatataatttatttactaggaattttat 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: 120 End: 149 .......................................................................................................................ATTGCAAAATATATAGGATTGGTATATAAT.................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ caccttttttactttgatttagcttattttttctatgtgaatctttacttgatataaaatctatcggattggcattgcaaaatatattgggttgatattcaaaaatctatcggattggcattgcaaaatatataggattggtatataatttatttactaggaattttat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1401:TDE1402|TDE1401:TDE1402:DedA family protein:hypothetical protein:->->:1443129..1443297 169 caccttttttactttgatttagcttattttttctatgtgaatctttacttgatataaaatctatcggattggcattgcaaaatatattgggttgatattcaaaaatctatcggattggcattgcaaaatatataggattggtatataatttatttactaggaattttat Intra-Species Hit: Count: 1 Min: 1 Max: 169 Len: 169 Subject: NC_002967_TDE1401_TDE1402|DedA family protein:hypothetical protein|POSITIVE:POSITIVE|[1443129,1443297]|169 HSP 1 e-value: 3.0E-91 bit: 335.0 Len: 169 Query Start:1 Query End:169 Subject Strand: POSITIVE Subject Start: 1 Subject End: 169 caccttttttactttgatttagcttattttttctatgtgaatctttacttgatataaaatctatcggattggcattgcaaaatatattgggttgatattcaaaaatctatcggattggcattgcaaaatatataggattggtatataatttatttactaggaattttat caccttttttactttgatttagcttattttttctatgtgaatctttacttgatataaaatctatcggattggcattgcaaaatatattgggttgatattcaaaaatctatcggattggcattgcaaaatatataggattggtatataatttatttactaggaattttat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CACCUUUUUUACUUUGAUUUAGCUUAUUUUUUCUAUGUGAAUCUUUACUUGAUAUAAAAUCUAUCGGAUUGGCAUUGCAAAAUAUAUUGGGUUGAUAUUCAAAAAUCUAUCGGAUUGGCAUUGCAAAAUAUAUAGGAUUGGUAUAUAAUUUAUUUACUAGGAAUUUUAU ..(((.........(((.(((...((((..(((((((((.........((((((.......))))))....(((.(((........((((((....)))))).((((.....)))).))).)))....)))))))))..))))..))).)))......)))........ (-26.16) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAAUUCCUAGUAAAUAAAUUAUAUACCAAUCCUAUAUAUUUUGCAAUGCCAAUCCGAUAGAUUUUUGAAUAUCAACCCAAUAUAUUUUGCAAUGCCAAUCCGAUAGAUUUUAUAUCAAGUAAAGAUUCACAUAGAAAAAAUAAGCUAAAUCAAAGUAAAAAAGGUG ............(((((.....((((((.......)))))).)))))...(((.....((((..........)))).........(((((((....((......((((.......)))).........(((.....))).......)).....))))))).....))). (-15.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 258 126 84 169 112 NC_002967:TDE0987|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1014041..1014271_POSITIVE 252 95 60 50 14 NC_002967:TDE0861|5end_tyrosyl-tRNA_synthetase_883098..883328_NEGATIVE 241 140 104 182 142 NC_002967:TDE0594|5end_cysteine_protease_domain,_YopT-type_634805..635035_NEGATIVE 236 120 72 107 61 NC_002967:TDE2753|5end_LysM_domain/M23/M37_peptidase_domain_protein_2810649..2810879_NEGATIVE 233 67 27 64 24 NC_002967:TDE0406|5end_hypothetical_protein_457230..457460_POSITIVE 224 120 71 76 34 NC_002967:TDE2045|5end_hypothetical_protein_2074933..2075163_NEGATIVE 221 120 71 90 50 NC_002967:TDE2131|5end_cobalamin_biosynthesis_protein_CbiM,_putative_2162683..2162913_NEGATIVE 218 120 74 187 149 NC_002967:TDE0839|5end_rhodanese-like_domain_protein_859341..859571_NEGATIVE 217 119 73 76 40 NC_002967:TDE0518|5end_hypothetical_protein_565263..565493_NEGATIVE 216 124 89 223 178 NC_002967:TDE1355|5end_hypothetical_protein_1395109..1395339_POSITIVE 214 114 72 193 151 NC_002967:TDE2129|5end_hypothetical_protein_2161463..2161693_POSITIVE 214 127 84 228 191 NC_002967:TDE1945|5end_hypothetical_protein_1961445..1961675_NEGATIVE 208 68 21 49 8 NC_002967:TDE1998|5end_phosphohexose_mutase_family_protein_2015300..2015530_POSITIVE 207 143 110 47 18 NC_002967:TDE0386|5end_ABC_transporter,_periplasmic_substrate-binding_protein_438321..438551_NEGATIVE 206 108 63 87 39 NC_002967:TDE2730|5end_hydrolase,_TatD_family_2786586..2786816_POSITIVE 205 115 71 99 56 NC_002967:TDE0389|5end_(R)-2-hydroxyglutaryl-CoA_dehydratase,_beta_subunit,_putative_440008..440238_POSITIVE 203 78 31 135 86 NC_002967:TDE0407|5end_glutamate_synthase_(NADPH),_homotetrameric_460522..460752_NEGATIVE 203 124 87 104 48 NC_002967:TDE0022|5end_hypothetical_protein_27872..28102_POSITIVE 202 129 82 64 17 NC_002967:TDE1102|5end_hypothetical_protein_1136175..1136405_NEGATIVE 201 93 55 218 171 NC_002967:TDE2121|5end_hypothetical_protein_2154729..2154959_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 241 140 104 149 109 NC_002967:TDE0595|3end_hypothetical_protein_634838..634988_NEGATIVE 218 120 74 109 71 NC_002967:TDE0840|3end_hypothetical_protein_859419..859569_NEGATIVE 207 146 108 91 52 NC_002967:TDE0010|3end_MutT/nudix_family_protein_15226..15376_POSITIVE 205 78 33 81 30 NC_002967:TDE0708|3end_nitroreductase_family_protein_744495..744645_POSITIVE 205 115 71 61 18 NC_002967:TDE0388|3end_hypothetical_protein_440050..440200_POSITIVE 203 102 61 41 1 NC_002967:TDE2402|3end_radical_SAM_domain_protein_2428664..2428814_POSITIVE 203 78 31 121 72 NC_002967:TDE0408|3end_oxidoreductase,_NAD-binding_460536..460686_NEGATIVE 200 149 106 141 100 NC_002967:TDE0954|3end_branched-chain_amino_acid_ABC_transporter,_permease_protein_978840..978990_POSITIVE 197 146 108 61 28 NC_002967:TDE1217|3end_flagellar_assembly_protein_1250517..1250667_POSITIVE 196 126 89 79 38 NC_002967:TDE1475|3end_flagellar_filament_core_protein_1521334..1521484_NEGATIVE 195 58 12 53 8 NC_002967:TDE0848|3end_hypothetical_protein_871558..871708_POSITIVE 190 143 101 62 30 NC_002967:TDE0817|3end_histidine_kinase-related_ATPase,_putative_839959..840109_POSITIVE 190 160 115 53 11 NC_002967:TDE0615|3end_cobalamin_biosynthesis_protein_CbiG_649856..650006_POSITIVE 189 140 98 65 19 NC_002967:TDE2250|3end_hypothetical_protein_2289409..2289559_POSITIVE 189 91 63 81 53 NC_002967:TDE0847|3end_hypothetical_protein_871342..871492_POSITIVE 189 70 22 122 67 NC_002967:TDE0534|3end_hypothetical_protein_577384..577534_POSITIVE 187 125 89 151 111 NC_002967:TDE1474|3end_hypothetical_protein_1521261..1521411_NEGATIVE 185 143 107 124 91 NC_002967:TDE0044|3end_ABC_transporter,_ATP-binding_protein_51660..51810_NEGATIVE 183 146 114 112 72 NC_002967:TDE1571|3end_hypothetical_protein_1620846..1620996_POSITIVE 183 48 3 85 35 NC_002967:TDE0767|3end_ribosomal_protein_L3_807061..807211_POSITIVE