Origin IGS: tgccatctactcctaaaacaaacatgattttgtctatttcaatcagttgtgcaaaacccttcaacaattctagtactttttatattttttttcaaggttcgaaaaattatatttttataatccttatgtcattaaattaaaaaagggatgctccttaaaggaacatcccttttgtttaagtgt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acacttaaacaaaagggatgttcctttaaggagcatcccttttttaatttaatgacataaggattataaaaatataatttttcgaaccttgaaaaaaaatataaaaagtactagaattgttgaagggttttgcacaactgattgaaatagacaaaatcatgtttgttttaggagtagatggca Mask Tandem Repeat Region ================================================ tgccatctactcctaaaacaaacatgattttgtctatttcaatcagttgtgcaaaacccttcaacaattctagtactttttatattttttttcaaggttcgaaaaattatatttttataatccttatgtcattaaattaaaaaagggatgctccttaaaggaacatcccttttgtttaagtgt Find is-nt database================================================ Query_seq: TDE1065:TDE1066|TDE1065:TDE1066:hypothetical protein:hypothetical protein:<-<-:1094242..1094424 183 tgccatctactcctaaaacaaacatgattttgtctatttcaatcagttgtgcaaaacccttcaacaattctagtactttttatattttttttcaaggttcgaaaaattatatttttataatccttatgtcattaaattaaaaaagggatgctccttaaaggaacatcccttttgtttaagtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1065:TDE1066|TDE1065:TDE1066:hypothetical protein:hypothetical protein:<-<-:1094242..1094424 183 tgccatctactcctaaaacaaacatgattttgtctatttcaatcagttgtgcaaaacccttcaacaattctagtactttttatattttttttcaaggttcgaaaaattatatttttataatccttatgtcattaaattaaaaaagggatgctccttaaaggaacatcccttttgtttaagtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1065:TDE1066|TDE1065:TDE1066:hypothetical protein:hypothetical protein:<-<-:1094242..1094424 183 tgccatctactcctaaaacaaacatgattttgtctatttcaatcagttgtgcaaaacccttcaacaattctagtactttttatattttttttcaaggttcgaaaaattatatttttataatccttatgtcattaaattaaaaaagggatgctccttaaaggaacatcccttttgtttaagtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgccatctactcctaaaacaaacatgattttgtctatttcaatcagttgtgcaaaacccttcaacaattctagtactttttatattttttttcaaggttcgaaaaattatatttttataatccttatgtcattaaattaaaaaagggatgctccttaaaggaacatcccttttgtttaagtgt Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 24 End: 137 ....................... M I L S I S I S C A K P F N N S S T F Y I F F Q G S K N Y I F I I L M S L N .............................................. tgccatctactcctaaaacaaacatgattttgtctatttcaatcagttgtgcaaaacccttcaacaattctagtactttttatattttttttcaaggttcgaaaaattatatttttataatccttatgtcattaaattaaaaaagggatgctccttaaaggaacatcccttttgtttaagtgt 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: 67 End: 96 ..................................................................CTTGAAAAAAAATATAAAAAGTACTAGAAT....................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgccatctactcctaaaacaaacatgattttgtctatttcaatcagttgtgcaaaacccttcaacaattctagtactttttatattttttttcaaggttcgaaaaattatatttttataatccttatgtcattaaattaaaaaagggatgctccttaaaggaacatcccttttgtttaagtgt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 70 HP_score: -8.3 Tail_Score: -2.71523 Start: 147 End: 167 Full_Region: TTAAATTAAAAAAGG GATGCTCCT TAA AGGAACATC CCTTTTGTTTAAGTG ..................................................................................................................................................GATGCTCCTTAAAGGAACATC................ Find igs database================================================ Query_seq: TDE1065:TDE1066|TDE1065:TDE1066:hypothetical protein:hypothetical protein:<-<-:1094242..1094424 183 tgccatctactcctaaaacaaacatgattttgtctatttcaatcagttgtgcaaaacccttcaacaattctagtactttttatattttttttcaaggttcgaaaaattatatttttataatccttatgtcattaaattaaaaaagggatgctccttaaaggaacatcccttttgtttaagtgt Intra-Species Hit: Count: 1 Min: 1 Max: 183 Len: 183 Subject: NC_002967_TDE1065_TDE1066|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1094242,1094424]|183 HSP 1 e-value: 3.0E-85 bit: 315.0 Len: 183 Query Start:1 Query End:183 Subject Strand: POSITIVE Subject Start: 1 Subject End: 183 tgccatctactcctaaaacaaacatgattttgtctatttcaatcagttgtgcaaaacccttcaacaattctagtactttttatannnnnnnncaaggttcgaaaaattatatttttataatccttatgtcattaaattaaaaaagggatgctccttaaaggaacatcccttttgtttaagtgt tgccatctactcctaaaacaaacatgattttgtctatttcaatcagttgtgcaaaacccttcaacaattctagtactttttatattttttttcaaggttcgaaaaattatatttttataatccttatgtcattaaattaaaaaagggatgctccttaaaggaacatcccttttgtttaagtgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCCAUCUACUCCUAAAACAAACAUGAUUUUGUCUAUUUCAAUCAGUUGUGCAAAACCCUUCAACAAUUCUAGUACUUUUUAUAUUUUUUUUCAAGGUUCGAAAAAUUAUAUUUUUAUAAUCCUUAUGUCAUUAAAUUAAAAAAGGGAUGCUCCUUAAAGGAACAUCCCUUUUGUUUAAGUGU ............((.((((..((((((..................((((............))))................((((..((((((.......))))))..))))...........))))))...........((((((((((.(((.....))).)))))))))))))).))... (-29.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACACUUAAACAAAAGGGAUGUUCCUUUAAGGAGCAUCCCUUUUUUAAUUUAAUGACAUAAGGAUUAUAAAAAUAUAAUUUUUCGAACCUUGAAAAAAAAUAUAAAAAGUACUAGAAUUGUUGAAGGGUUUUGCACAACUGAUUGAAAUAGACAAAAUCAUGUUUGUUUUAGGAGUAGAUGGCA .((.(((((.((((((((((((((.....))))))))))))))....)))))))....((((((((((....)))))))))).(((((((..((...(((.((........))..))).))..))))))).((.((.(((.((((((((((((......))))))))))))...))).)))). (-44.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 784 50 1 141 92 NC_002967:TDE1065|5end_hypothetical_protein_1094151..1094381_NEGATIVE 272 179 139 150 112 NC_002967:TDE1910|5end_1-deoxy-D-xylulose-5-phosphate_synthase_1928837..1929067_NEGATIVE 263 180 145 216 184 NC_002967:TDE0741|5end_hypothetical_protein_778158..778388_NEGATIVE 255 79 37 121 86 NC_002967:TDE0486|5end_hypothetical_protein_543612..543842_NEGATIVE 244 175 145 143 115 NC_002967:TDE2265|5end_hypothetical_protein_2302165..2302395_POSITIVE 233 168 144 47 20 NC_002967:TDE2421|5end_DNA-directed_RNA_polymerase_beta_subunit_2452762..2452992_NEGATIVE 231 95 51 103 57 NC_002967:TDE2200|5end_methionine_gamma-lyase_2238455..2238685_NEGATIVE 228 177 147 56 29 NC_002967:TDE0203|5end_hypothetical_protein_236670..236900_POSITIVE 227 177 146 178 143 NC_002967:TDE0979|5end_penicillin_binding_protein_1003946..1004176_NEGATIVE 227 179 144 203 169 NC_002967:TDE0619|5end_methyl-accepting_chemotaxis_protein_650318..650548_POSITIVE 222 173 145 126 85 NC_002967:TDE1949|5end_ABC_transporter,_ATP-binding_protein_1966067..1966297_NEGATIVE 216 175 142 226 194 NC_002967:TDE1058|5end_hypothetical_protein_1086366..1086596_NEGATIVE 216 94 51 187 133 NC_002967:TDE0073|5end_riboflavin_biosynthesis_protein_RibF,_putative_84082..84312_NEGATIVE 215 177 143 87 52 NC_002967:TDE0531|5end_hypothetical_protein_574874..575104_POSITIVE 213 103 72 199 169 NC_002967:TDE1278|5end_conserved_hypothetical_protein_TIGR01440_1312788..1313018_NEGATIVE 212 70 21 97 50 NC_002967:TDE0830|5end_hypothetical_protein_852025..852255_NEGATIVE 209 90 41 160 114 NC_002967:TDE1420|5end_hypothetical_protein_1464375..1464605_POSITIVE 209 170 150 124 103 NC_002967:TDE0860|5end_ribosomal_small_subunit_pseudouridine_synthase_A_881023..881253_POSITIVE 208 156 119 120 79 NC_002967:TDE1900|5end_hypothetical_protein_1921124..1921354_POSITIVE 205 69 30 84 42 NC_002967:TDE0248|5end_hypothetical_protein_282068..282298_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 272 179 139 44 6 NC_002967:TDE1911|3end_hypothetical_protein_1928943..1929093_NEGATIVE 255 79 37 105 70 NC_002967:TDE0487|3end_ABC_transporter,_ATP-binding_protein_543628..543778_NEGATIVE 251 169 124 65 24 NC_002967:TDE1296|3end_ribosomal_subunit_interface_protein,_putative_1333464..1333614_NEGATIVE 247 178 135 115 68 NC_002967:TDE1914|3end_Holliday_junction_DNA_helicase_RuvB_1930889..1931039_NEGATIVE 242 172 142 78 49 NC_002967:TDE1133|3end_hypothetical_protein_1164753..1164903_NEGATIVE 231 95 51 66 20 NC_002967:TDE2201|3end_hypothetical_protein_2238492..2238642_NEGATIVE 227 177 146 145 110 NC_002967:TDE0980|3end_asparaginyl-tRNA_synthetase_1003979..1004129_NEGATIVE 225 177 145 70 38 NC_002967:TDE2028|3end_OmpA_family_protein_2057019..2057169_POSITIVE 216 175 142 94 62 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE 216 94 51 113 59 NC_002967:TDE0074|3end_amino_acid_permease_family_protein_84156..84306_NEGATIVE 215 174 139 88 55 NC_002967:TDE1048|3end_30S_ribosomal_protein_S7_1075032..1075182_POSITIVE 214 173 145 37 9 NC_002967:TDE0026|3end_TraB_family_protein_31826..31976_NEGATIVE 209 170 150 127 106 NC_002967:TDE0859|3end_hypothetical_protein_881106..881256_POSITIVE 203 174 136 96 52 NC_002967:TDE0658|3end_ABC_transporter,_permease_protein_695679..695829_POSITIVE 201 75 41 112 80 NC_002967:TDE0826|3end_hypothetical_protein_847860..848010_POSITIVE 199 68 41 139 112 NC_002967:TDE1419|3end_glycosyl_transferase,_group_2_family_protein_1464453..1464603_POSITIVE 197 156 121 122 88 NC_002967:TDE1150|3end_hypothetical_protein_1187401..1187551_NEGATIVE 197 177 144 86 49 NC_002967:TDE0659|3end_hypothetical_protein_695690..695840_NEGATIVE 197 100 58 144 94 NC_002967:TDE0603|3end_hypothetical_protein_641885..642035_POSITIVE 196 108 68 43 3 NC_002967:TDE1163|3end_hypothetical_protein_1197700..1197850_NEGATIVE