Origin IGS: ctctatttaaaatgaaattttggcacaatagtgctttttgtcgcgatttcatttacgttttctgtgtttaaaaatcaaaaatctgtttattttaattatttcgattttataattctatatccaatataaaattataaaatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aattttataattttatattggatatagaattataaaatcgaaataattaaaataaacagatttttgatttttaaacacagaaaacgtaaatgaaatcgcgacaaaaagcactattgtgccaaaatttcattttaaatagag Mask Tandem Repeat Region ================================================ ctctatttaaaatgaaattttggcacaatagtgctttttgtcgcgatttcatttacgttttctgtgtttaaaaatcaaaaatctgtttattttaattatttcgattttataattctatatccaatataaaattataaaatt Find is-nt database================================================ Query_seq: TDE1027:TDE1028|TDE1027:TDE1028:ribonuclease III:hypothetical protein:->->:1058443..1058583 141 ctctatttaaaatgaaattttggcacaatagtgctttttgtcgcgatttcatttacgttttctgtgtttaaaaatcaaaaatctgtttattttaattatttcgattttataattctatatccaatataaaattataaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1027:TDE1028|TDE1027:TDE1028:ribonuclease III:hypothetical protein:->->:1058443..1058583 141 ctctatttaaaatgaaattttggcacaatagtgctttttgtcgcgatttcatttacgttttctgtgtttaaaaatcaaaaatctgtttattttaattatttcgattttataattctatatccaatataaaattataaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1027:TDE1028|TDE1027:TDE1028:ribonuclease III:hypothetical protein:->->:1058443..1058583 141 ctctatttaaaatgaaattttggcacaatagtgctttttgtcgcgatttcatttacgttttctgtgtttaaaaatcaaaaatctgtttattttaattatttcgattttataattctatatccaatataaaattataaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctctatttaaaatgaaattttggcacaatagtgctttttgtcgcgatttcatttacgttttctgtgtttaaaaatcaaaaatctgtttattttaattatttcgattttataattctatatccaatataaaattataaaatt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 28 End: 126 ........................... M V L F V A I S F T F S V F K N Q K S V Y F N Y F D F I I L Y P I ............... ctctatttaaaatgaaattttggcacaatagtgctttttgtcgcgatttcatttacgttttctgtgtttaaaaatcaaaaatctgtttattttaattatttcgattttataattctatatccaatataaaattataaaatt 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================================================ ctctatttaaaatgaaattttggcacaatagtgctttttgtcgcgatttcatttacgttttctgtgtttaaaaatcaaaaatctgtttattttaattatttcgattttataattctatatccaatataaaattataaaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1027:TDE1028|TDE1027:TDE1028:ribonuclease III:hypothetical protein:->->:1058443..1058583 141 ctctatttaaaatgaaattttggcacaatagtgctttttgtcgcgatttcatttacgttttctgtgtttaaaaatcaaaaatctgtttattttaattatttcgattttataattctatatccaatataaaattataaaatt Intra-Species Hit: Count: 1 Min: 1 Max: 141 Len: 141 Subject: NC_002967_TDE1027_TDE1028|ribonuclease III:hypothetical protein|POSITIVE:POSITIVE|[1058443,1058583]|141 HSP 1 e-value: 1.0E-74 bit: 280.0 Len: 141 Query Start:1 Query End:141 Subject Strand: POSITIVE Subject Start: 1 Subject End: 141 ctctatttaaaatgaaattttggcacaatagtgctttttgtcgcgatttcatttacgttttctgtgtttaaaaatcaaaaatctgtttattttaattatttcgattttataattctatatccaatataaaattataaaatt ctctatttaaaatgaaattttggcacaatagtgctttttgtcgcgatttcatttacgttttctgtgtttaaaaatcaaaaatctgtttattttaattatttcgattttataattctatatccaatataaaattataaaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCUAUUUAAAAUGAAAUUUUGGCACAAUAGUGCUUUUUGUCGCGAUUUCAUUUACGUUUUCUGUGUUUAAAAAUCAAAAAUCUGUUUAUUUUAAUUAUUUCGAUUUUAUAAUUCUAUAUCCAAUAUAAAAUUAUAAAAUU ......((((((((((.....(((((....))))).........(((((....((((.....)))).....))))).........)))))))))).......((((((((((((.(((((...))))).)))))))))))) (-22.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUUAUAAUUUUAUAUUGGAUAUAGAAUUAUAAAAUCGAAAUAAUUAAAAUAAACAGAUUUUUGAUUUUUAAACACAGAAAACGUAAAUGAAAUCGCGACAAAAAGCACUAUUGUGCCAAAAUUUCAUUUUAAAUAGAG .(((((((((((((((((...))))))))))))))))).(((((.....................((((((.....((.......))....))))))..........((((....))))....)))))............. (-21.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 247 69 21 198 131 NC_002967:TDE2125|5end_leucyl/phenylalanyl-tRNA--protein_transferase_2158711..2158941_POSITIVE 238 69 21 217 166 NC_002967:TDE0515|5end_hypothetical_protein_563783..564013_NEGATIVE 230 68 22 96 33 NC_002967:TDE2191|5end_pyrimidine-nucleoside_phosphorylase_2227651..2227881_NEGATIVE 226 65 23 63 21 NC_002967:TDE1595|5end_cobalamin_biosynthesis_protein_CbiD_1646039..1646269_NEGATIVE 225 67 30 68 36 NC_002967:TDE2620|5end_hypothetical_protein_2661538..2661768_POSITIVE 224 55 30 30 2 NC_002967:TDE0283|5end_transporter,_putative_312825..313055_NEGATIVE 223 65 35 61 31 NC_002967:TDE1840|5end_hypothetical_protein_1871581..1871811_NEGATIVE 223 65 35 61 31 NC_002967:TDE1800|5end_hypothetical_protein_1837684..1837914_NEGATIVE 222 69 29 185 141 NC_002967:TDE0429|5end_hypothetical_protein_485423..485653_NEGATIVE 215 65 21 131 85 NC_002967:TDE1878|5end_hydrolase,_haloacid_dehalogenase-like_family_1900745..1900975_NEGATIVE 215 69 21 213 162 NC_002967:TDE0790|5end_30S_ribosomal_protein_S11_816951..817181_POSITIVE 214 69 21 59 11 NC_002967:TDE1405|5end_phosphoribosylformylglycinamidine_synthetase_I_1448674..1448904_NEGATIVE 213 69 22 81 39 NC_002967:TDE2636|5end_hypothetical_protein_2676070..2676300_POSITIVE 213 56 19 151 113 NC_002967:TDE1996|5end_hypothetical_protein_2014243..2014473_POSITIVE 213 69 23 151 100 NC_002967:TDE1911|5end_hypothetical_protein_1929098..1929328_NEGATIVE 212 66 28 71 30 NC_002967:TDE2172|5end_hypothetical_protein_2202768..2202998_NEGATIVE 212 66 24 168 122 NC_002967:TDE0909|5end_type_II_DNA_modification_methyltransferase_M.TdeIII_927166..927396_POSITIVE 212 67 32 76 42 NC_002967:TDE0666|5end_FeS_assembly_ATPase_SufC_703553..703783_POSITIVE 212 62 27 170 126 NC_002967:TDE0166|5end_hypothetical_protein_195871..196101_NEGATIVE 210 70 30 169 134 NC_002967:TDE2275|5end_tRNA_pseudouridine_synthase_A_2311076..2311306_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 263 69 22 54 6 NC_002967:TDE2621|3end_hypothetical_protein_2662197..2662347_POSITIVE 239 57 19 151 101 NC_002967:TDE2124|3end_ATP-dependent_Clp_protease,_ATP-binding_subunit_ClpA_2158763..2158913_POSITIVE 229 68 34 70 31 NC_002967:TDE0501|3end_hypothetical_protein_554185..554335_NEGATIVE 224 55 30 29 1 NC_002967:TDE0284|3end_hypothetical_protein_312826..312976_NEGATIVE 223 65 35 71 41 NC_002967:TDE1841|3end_hypothetical_protein_1871571..1871721_NEGATIVE 223 65 35 71 41 NC_002967:TDE1801|3end_hypothetical_protein_1837674..1837824_NEGATIVE 214 69 21 56 8 NC_002967:TDE1406|3end_hypothetical_protein_1448677..1448827_NEGATIVE 213 56 19 72 34 NC_002967:TDE1995|3end_magnesium_chelatase_family_protein_2014244..2014394_POSITIVE 212 66 28 102 61 NC_002967:TDE2173|3end_hypothetical_protein_2202737..2202887_NEGATIVE 208 69 26 64 25 NC_002967:TDE1658|3end_basic_membrane_protein,_putative_1707655..1707805_NEGATIVE 200 56 18 74 38 NC_002967:TDE0042|3end_phosphate_acetyltransferase_49763..49913_POSITIVE 198 70 26 66 26 NC_002967:TDE0689|3end_5-methylthioribose_kinase_726972..727122_POSITIVE 195 69 22 100 56 NC_002967:TDE1894|3end_ferredoxin_1915041..1915191_POSITIVE 192 65 32 108 79 NC_002967:TDE1140|3end_hypothetical_protein_1168730..1168880_NEGATIVE 191 65 21 80 25 NC_002967:TDE2222|3end_hypothetical_protein_2264702..2264852_POSITIVE 191 65 26 140 92 NC_002967:TDE1170|3end_DNA-binding_protein_1200242..1200392_POSITIVE 191 68 41 31 6 NC_002967:TDE0795|3end_hypothetical_protein_819588..819738_NEGATIVE 190 64 30 112 71 NC_002967:TDE1605|3end_hypothetical_protein_1655533..1655683_NEGATIVE 189 62 21 132 85 NC_002967:TDE0136|3end_hypothetical_protein_156723..156873_POSITIVE 188 57 11 148 103 NC_002967:TDE1676|3end_ribosomal_protein_S18_1729373..1729523_NEGATIVE