Origin IGS: tatattccgctcaaatctaaaaaaaaggggcttcaaagctgagccccccttccgtttaaccgaaagctatagatatttgaacaattaggggtataccctcctaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attaggagggtatacccctaattgttcaaatatctatagctttcggttaaacggaaggggggctcagctttgaagccccttttttttagatttgagcggaatata Mask Tandem Repeat Region ================================================ tatattccgctcaaatctaaaaaaaaggggcttcaaagctgagccccccttccgtttaaccgaaagctatagatatttgaacaattaggggtataccctcctaat Find is-nt database================================================ Query_seq: TDE1910:TDE1911|TDE1910:TDE1911:1-deoxy-D-xylulose-5-phosphate synthase:hypothetical protein:<-<-:1928928..1929032 105 tatattccgctcaaatctaaaaaaaaggggcttcaaagctgagccccccttccgtttaaccgaaagctatagatatttgaacaattaggggtataccctcctaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1910:TDE1911|TDE1910:TDE1911:1-deoxy-D-xylulose-5-phosphate synthase:hypothetical protein:<-<-:1928928..1929032 105 tatattccgctcaaatctaaaaaaaaggggcttcaaagctgagccccccttccgtttaaccgaaagctatagatatttgaacaattaggggtataccctcctaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1910:TDE1911|TDE1910:TDE1911:1-deoxy-D-xylulose-5-phosphate synthase:hypothetical protein:<-<-:1928928..1929032 105 tatattccgctcaaatctaaaaaaaaggggcttcaaagctgagccccccttccgtttaaccgaaagctatagatatttgaacaattaggggtataccctcctaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatattccgctcaaatctaaaaaaaaggggcttcaaagctgagccccccttccgtttaaccgaaagctatagatatttgaacaattaggggtataccctcctaat Predict ORF larger than 30AA ================================================ tatattccgctcaaatctaaaaaaaaggggcttcaaagctgagccccccttccgtttaaccgaaagctatagatatttgaacaattaggggtataccctcctaat 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================================================ tatattccgctcaaatctaaaaaaaaggggcttcaaagctgagccccccttccgtttaaccgaaagctatagatatttgaacaattaggggtataccctcctaat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -7.6 Tail_Score: -5.89947 Start: 27 End: 47 Full_Region: cggttaaacggaagg ggggctca gctt tgaagcccc ttttttttagatttg ..........................ggggctcagctttgaagcccc.......................................................... Find igs database================================================ Query_seq: TDE1910:TDE1911|TDE1910:TDE1911:1-deoxy-D-xylulose-5-phosphate synthase:hypothetical protein:<-<-:1928928..1929032 105 tatattccgctcaaatctaaaaaaaaggggcttcaaagctgagccccccttccgtttaaccgaaagctatagatatttgaacaattaggggtataccctcctaat Intra-Species Hit: Count: 1 Min: 1 Max: 105 Len: 105 Subject: NC_002967_TDE1910_TDE1911|1-deoxy-D-xylulose-5-phosphate synthase:hypothetical protein|NEGATIVE:NEGATIVE|[1928928,1929032]|105 HSP 1 e-value: 5.0E-39 bit: 161.0 Len: 105 Query Start:1 Query End:105 Subject Strand: POSITIVE Subject Start: 1 Subject End: 105 tatattccgctcaaatctnnnnnnnnggggcttcaaagctgagccccccttccgtttaaccgaaagctatagatatttgaacaattaggggtataccctcctaat tatattccgctcaaatctaaaaaaaaggggcttcaaagctgagccccccttccgtttaaccgaaagctatagatatttgaacaattaggggtataccctcctaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAUUCCGCUCAAAUCUAAAAAAAAGGGGCUUCAAAGCUGAGCCCCCCUUCCGUUUAACCGAAAGCUAUAGAUAUUUGAACAAUUAGGGGUAUACCCUCCUAAU ........(.(((((((((.......((((((.((....))))))))......((((......))))..)))))..)))).).((((((((......)))))))) (-25.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAGGAGGGUAUACCCCUAAUUGUUCAAAUAUCUAUAGCUUUCGGUUAAACGGAAGGGGGGCUCAGCUUUGAAGCCCCUUUUUUUUAGAUUUGAGCGGAAUAUA ((((((.((.....)))))))).((((((..(((((...((((((......)))))).(((((((......).)))))).......)))))))))))........ (-35.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 965 70 21 161 112 NC_002967:TDE1910|5end_1-deoxy-D-xylulose-5-phosphate_synthase_1928837..1929067_NEGATIVE 340 68 27 218 177 NC_002967:TDE2393|5end_hypothetical_protein_2422398..2422628_POSITIVE 328 63 26 64 27 NC_002967:TDE0693|5end_phosphomethylpyrimidine_kinase_729942..730172_POSITIVE 297 73 31 214 162 NC_002967:TDE1261|5end_choline/carnitine/betaine_transporter_family_protein_1295593..1295823_POSITIVE 297 63 27 57 9 NC_002967:TDE0135|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_154927..155157_POSITIVE 293 63 27 231 198 NC_002967:TDE2644|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_2683651..2683881_POSITIVE 291 68 23 62 8 NC_002967:TDE2447|5end_shikimate_kinase_2476928..2477158_NEGATIVE 290 68 37 165 127 NC_002967:TDE1043|5end_hypothetical_protein_1070945..1071175_POSITIVE 287 49 2 229 164 NC_002967:TDE0979|5end_penicillin_binding_protein_1003946..1004176_NEGATIVE 287 69 25 90 48 NC_002967:TDE0606|5end_ParB_family_protein_644132..644362_NEGATIVE 283 67 26 143 103 NC_002967:TDE1330|5end_conserved_hypothetical_protein_TIGR00244_1365379..1365609_POSITIVE 281 67 31 80 38 NC_002967:TDE1267|5end_phosphoribosylamine--glycine_ligase_1302940..1303170_NEGATIVE 278 70 21 161 103 NC_002967:TDE0797|5end_acylphosphatase_820859..821089_POSITIVE 276 69 25 192 142 NC_002967:TDE2697|5end_3-oxo-5-alpha-steroid_4-dehydrogenase_family_protein_2740260..2740490_POSITIVE 276 70 28 46 7 NC_002967:TDE0370|5end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_421084..421314_POSITIVE 272 67 26 138 93 NC_002967:TDE2632|5end_peptide_ABC_transporter,_ATP-binding_protein,_putative_2672650..2672880_POSITIVE 265 67 26 217 167 NC_002967:TDE2347|5end_30S_ribosomal_protein_S2_2384378..2384608_NEGATIVE 265 61 27 41 9 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 265 70 26 180 141 NC_002967:TDE0248|5end_hypothetical_protein_282068..282298_POSITIVE 264 72 38 201 155 NC_002967:TDE2428|5end_ribosomal_protein_L33_2456292..2456522_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 352 61 31 146 117 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 336 65 26 100 44 NC_002967:TDE0479|3end_hydroxylamine_reductase_535029..535179_NEGATIVE 311 68 29 46 7 NC_002967:TDE1386|3end_methyl-accepting_chemotaxis_protein_1426856..1427006_POSITIVE 300 62 24 139 76 NC_002967:TDE0824|3end_lipoprotein,_putative_845226..845376_NEGATIVE 297 63 27 60 12 NC_002967:TDE0134|3end_oxidoreductase,_FAD-dependent_155010..155160_POSITIVE 290 68 37 146 108 NC_002967:TDE1042|3end_deoxyuridine_5'triphosphate_nucleotidohydrolase_1071006..1071156_POSITIVE 287 69 25 97 55 NC_002967:TDE0607|3end_ParA_family_ATPase_644125..644275_NEGATIVE 281 67 27 84 36 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 274 67 21 95 46 NC_002967:TDE1066|3end_hypothetical_protein_1094335..1094485_NEGATIVE 273 51 27 87 59 NC_002967:TDE1691|3end_hypothetical_protein_1747407..1747557_NEGATIVE 272 67 26 141 96 NC_002967:TDE2631|3end_peptide_ABC_transporter,_permease_protein,_putative_2672733..2672883_POSITIVE 271 70 26 115 53 NC_002967:TDE0621|3end_MATE_efflux_family_protein_654776..654926_POSITIVE 270 68 26 57 12 NC_002967:TDE0434|3end_rubrerythrin_489564..489714_POSITIVE 269 47 11 79 45 NC_002967:TDE1188|3end_NAD(P)_transhydrogenase,_beta_subunit_1214574..1214724_NEGATIVE 269 49 2 148 101 NC_002967:TDE0796|3end_histidinol_phosphate_phosphatase_HisJ_family_protein_820946..821096_POSITIVE 268 68 21 115 55 NC_002967:TDE1048|3end_30S_ribosomal_protein_S7_1075032..1075182_POSITIVE 267 68 23 76 37 NC_002967:TDE0870|3end_phosphatase/nucleotidase_894676..894826_POSITIVE 267 63 27 146 114 NC_002967:TDE0636|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_670532..670682_NEGATIVE 265 61 27 69 37 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 263 51 11 50 2 NC_002967:TDE0239|3end_glycine_reductase_complex_protein_GrdD_271828..271978_NEGATIVE