Origin IGS: gttttgactatacaataatttttagcttaggtcaacagatttattaggattaaaattttgctatttattgaaaacaatttctataataattatgaaaggggaaaatttttcttcttttcaaataatttttattagaggtaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttttacctctaataaaaattatttgaaaagaagaaaaattttcccctttcataattattatagaaattgttttcaataaatagcaaaattttaatcctaataaatctgttgacctaagctaaaaattattgtatagtcaaaac Mask Tandem Repeat Region ================================================ gttttgactatacaataatttttagcttaggtcaacagatttattaggattaaaattttgctatttattgaaaacaatttctataataattatgaaaggggaaaatttttcttcttttcaaataatttttattagaggtaaaa Find is-nt database================================================ Query_seq: TDE0861:TDE0862|TDE0861:TDE0862:tyrosyl-tRNA synthetase:hypothetical protein:<-->:883189..883331 143 gttttgactatacaataatttttagcttaggtcaacagatttattaggattaaaattttgctatttattgaaaacaatttctataataattatgaaaggggaaaatttttcttcttttcaaataatttttattagaggtaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0861:TDE0862|TDE0861:TDE0862:tyrosyl-tRNA synthetase:hypothetical protein:<-->:883189..883331 143 gttttgactatacaataatttttagcttaggtcaacagatttattaggattaaaattttgctatttattgaaaacaatttctataataattatgaaaggggaaaatttttcttcttttcaaataatttttattagaggtaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0861:TDE0862|TDE0861:TDE0862:tyrosyl-tRNA synthetase:hypothetical protein:<-->:883189..883331 143 gttttgactatacaataatttttagcttaggtcaacagatttattaggattaaaattttgctatttattgaaaacaatttctataataattatgaaaggggaaaatttttcttcttttcaaataatttttattagaggtaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gttttgactatacaataatttttagcttaggtcaacagatttattaggattaaaattttgctatttattgaaaacaatttctataataattatgaaaggggaaaatttttcttcttttcaaataatttttattagaggtaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 43 End: 132 .......................................... M R I K I L L F I E N N F Y N N Y E R G K F F F F S N N F Y ........... gttttgactatacaataatttttagcttaggtcaacagatttattaggattaaaattttgctatttattgaaaacaatttctataataattatgaaaggggaaaatttttcttcttttcaaataatttttattagaggtaaaa 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: 86 Start: 7 End: 36 ......GTTGACCTAAGCTAAAAATTATTGTATAGT........................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gttttgactatacaataatttttagcttaggtcaacagatttattaggattaaaattttgctatttattgaaaacaatttctataataattatgaaaggggaaaatttttcttcttttcaaataatttttattagaggtaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0861:TDE0862|TDE0861:TDE0862:tyrosyl-tRNA synthetase:hypothetical protein:<-->:883189..883331 143 gttttgactatacaataatttttagcttaggtcaacagatttattaggattaaaattttgctatttattgaaaacaatttctataataattatgaaaggggaaaatttttcttcttttcaaataatttttattagaggtaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 143 Len: 143 Subject: NC_002967_TDE0861_TDE0862|tyrosyl-tRNA synthetase:hypothetical protein|NEGATIVE:POSITIVE|[883189,883331]|143 HSP 1 e-value: 8.0E-76 bit: 283.0 Len: 143 Query Start:1 Query End:143 Subject Strand: POSITIVE Subject Start: 1 Subject End: 143 gttttgactatacaataatttttagcttaggtcaacagatttattaggattaaaattttgctatttattgaaaacaatttctataataattatgaaaggggaaaatttttcttcttttcaaataatttttattagaggtaaaa gttttgactatacaataatttttagcttaggtcaacagatttattaggattaaaattttgctatttattgaaaacaatttctataataattatgaaaggggaaaatttttcttcttttcaaataatttttattagaggtaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUUGACUAUACAAUAAUUUUUAGCUUAGGUCAACAGAUUUAUUAGGAUUAAAAUUUUGCUAUUUAUUGAAAACAAUUUCUAUAAUAAUUAUGAAAGGGGAAAAUUUUUCUUCUUUUCAAAUAAUUUUUAUUAGAGGUAAAA ............((((((....((((.((((((....))))))................)))).))))))......((((((((((.((((((((((((((((.....))))))))))...)))))).))).))))))).... (-23.33) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUACCUCUAAUAAAAAUUAUUUGAAAAGAAGAAAAAUUUUCCCCUUUCAUAAUUAUUAUAGAAAUUGUUUUCAAUAAAUAGCAAAAUUUUAAUCCUAAUAAAUCUGUUGACCUAAGCUAAAAAUUAUUGUAUAGUCAAAAC .......((((.(((.(((((..(((((.(((((....)))))...)))))))))).)))))))..(((((..........)))))......................(((((.((.((...........)).)))))))... (-12.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 715 50 1 141 92 NC_002967:TDE0861|5end_tyrosyl-tRNA_synthetase_883098..883328_NEGATIVE 513 100 53 211 164 NC_002967:TDE0670|5end_ATP-dependent_protease_La_707938..708168_POSITIVE 453 98 53 231 186 NC_002967:TDE2718|5end_magnesium_transporter_2775910..2776140_NEGATIVE 399 127 81 144 99 NC_002967:TDE1692|5end_hypothetical_protein_1748293..1748523_POSITIVE 392 117 82 193 157 NC_002967:TDE0402|5end_hypothetical_protein_454352..454582_NEGATIVE 384 109 61 231 182 NC_002967:TDE0164|5end_hypothetical_protein_193998..194228_NEGATIVE 379 128 82 67 22 NC_002967:TDE2099|5end_hypothetical_protein_2125027..2125257_POSITIVE 314 120 75 142 96 NC_002967:TDE0165|5end_hypothetical_protein_194122..194352_POSITIVE 293 120 75 141 96 NC_002967:TDE2719|5end_hypothetical_protein_2776045..2776275_POSITIVE 288 120 72 140 95 NC_002967:TDE2136|5end_hypothetical_protein_2165659..2165889_NEGATIVE 248 86 44 187 145 NC_002967:TDE1990|5end_ATP-dependent_helicase,_DinG_family_2008496..2008726_NEGATIVE 247 120 73 142 96 NC_002967:TDE2707|5end_hypothetical_protein_2753947..2754177_POSITIVE 245 120 76 139 96 NC_002967:TDE0049|5end_hypothetical_protein_59089..59319_NEGATIVE 234 120 77 143 97 NC_002967:TDE0007|5end_hypothetical_protein_9874..10104_POSITIVE 224 139 95 159 118 NC_002967:TDE1344|5end_hypothetical_protein_1382392..1382622_POSITIVE 209 120 77 141 96 NC_002967:TDE1691|5end_hypothetical_protein_1748273..1748503_NEGATIVE 203 80 49 231 200 NC_002967:TDE2706|5end_hypothetical_protein_2753793..2754023_NEGATIVE 198 120 72 141 95 NC_002967:TDE2098|5end_hypothetical_protein_2125085..2125315_NEGATIVE 194 130 83 87 39 NC_002967:TDE0394|5end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_443981..444211_POSITIVE 192 68 22 136 91 NC_002967:TDE0629|5end_chaperone_protein_DnaJ_662587..662817_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 248 86 44 49 7 NC_002967:TDE1991|3end_hypothetical_protein_2008634..2008784_NEGATIVE 232 70 21 55 3 NC_002967:TDE2295|3end_mechanosensitive_ion_channel_family_protein_2334283..2334433_POSITIVE 192 68 22 98 53 NC_002967:TDE0628|3end_molecular_chaperone_DnaK_662629..662779_POSITIVE 185 111 81 92 64 NC_002967:TDE0323|3end_hypothetical_protein_355750..355900_NEGATIVE 180 140 91 139 72 NC_002967:TDE0457|3end_hypothetical_protein_514129..514279_POSITIVE 179 68 24 101 55 NC_002967:TDE1409|3end_flagellar_filament_outer_layer_protein_FlaA,_putative_1452381..1452531_POSITIVE 173 70 26 110 50 NC_002967:TDE1007|3end_flagellar_basal-body_rod_protein_FlgG_1032135..1032285_POSITIVE 173 33 11 123 103 NC_002967:TDE0139|3end_hypothetical_protein_160121..160271_NEGATIVE 171 41 7 77 47 NC_002967:TDE0213|3end_TPR_domain_protein_248318..248468_NEGATIVE 169 61 24 79 40 NC_002967:TDE1661|3end_hypothetical_protein_1715910..1716060_POSITIVE 168 129 90 89 49 NC_002967:TDE1971|3end_DNA_polymerase_III_domain_protein_1985741..1985891_NEGATIVE 163 71 37 112 67 NC_002967:TDE0188|3end_adenosine_deaminase_225700..225850_POSITIVE 160 70 30 110 65 NC_002967:TDE0281|3end_hypothetical_protein_310293..310443_NEGATIVE 160 100 58 86 42 NC_002967:TDE0088|3end_Trk_system_potassium_uptake_protein_TrkH_106869..107019_POSITIVE 159 41 22 41 15 NC_002967:TDE2641|3end_Fic_family_protein_2682068..2682218_POSITIVE 159 128 93 92 62 NC_002967:TDE1893|3end_GTP-binding_protein_LepA_1912212..1912362_NEGATIVE 158 140 98 67 28 NC_002967:TDE1355|3end_hypothetical_protein_1395527..1395677_POSITIVE 153 74 45 49 15 NC_002967:TDE2059|3end_hypothetical_protein_2086309..2086459_NEGATIVE 152 62 24 91 46 NC_002967:TDE1631|3end_citrate_lyase,_alpha_subunit_1680060..1680210_NEGATIVE 152 108 74 71 29 NC_002967:TDE0005|3end_L-threonine_aldolase,_low-specificity_4985..5135_NEGATIVE