Origin IGS: tttagctctccttaagaatctatattaatttattaattatcgtgggtataagatacaaaaaaaacggcaaaacggcaagggggtaggggaattgcctttatgccgcttccttctttaattctttttgtta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taacaaaaagaattaaagaaggaagcggcataaaggcaattcccctacccccttgccgttttgccgttttttttgtatcttatacccacgataattaataaattaatatagattcttaaggagagctaaa Mask Tandem Repeat Region ================================================ tttagctctccttaagaatctatattaatttattaattatcgtgggtataagatacaaaaaaaacggcaaaacggcaagggggtaggggaattgcctttatgccgcttccttctttaattctttttgtta Find is-nt database================================================ Query_seq: TDE1175:TDE1176|TDE1175:TDE1176:chaperonin GroEL:oxygen-independent coproporphyrinogen III oxidase, putative:<-<-:1205242..1205371 130 tttagctctccttaagaatctatattaatttattaattatcgtgggtataagatacaaaaaaaacggcaaaacggcaagggggtaggggaattgcctttatgccgcttccttctttaattctttttgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1175:TDE1176|TDE1175:TDE1176:chaperonin GroEL:oxygen-independent coproporphyrinogen III oxidase, putative:<-<-:1205242..1205371 130 tttagctctccttaagaatctatattaatttattaattatcgtgggtataagatacaaaaaaaacggcaaaacggcaagggggtaggggaattgcctttatgccgcttccttctttaattctttttgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1175:TDE1176|TDE1175:TDE1176:chaperonin GroEL:oxygen-independent coproporphyrinogen III oxidase, putative:<-<-:1205242..1205371 130 tttagctctccttaagaatctatattaatttattaattatcgtgggtataagatacaaaaaaaacggcaaaacggcaagggggtaggggaattgcctttatgccgcttccttctttaattctttttgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttagctctccttaagaatctatattaatttattaattatcgtgggtataagatacaaaaaaaacggcaaaacggcaagggggtaggggaattgcctttatgccgcttccttctttaattctttttgtta Predict ORF larger than 30AA ================================================ tttagctctccttaagaatctatattaatttattaattatcgtgggtataagatacaaaaaaaacggcaaaacggcaagggggtaggggaattgcctttatgccgcttccttctttaattctttttgtta 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: 83 Start: 50 End: 79 .................................................CTTGCCGTTTTGCCGTTTTTTTTGTATCTT................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttagctctccttaagaatctatattaatttattaattatcgtgggtataagatacaaaaaaaacggcaaaacggcaagggggtaggggaattgcctttatgccgcttccttctttaattctttttgtta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 90 HP_score: -2.6 Tail_Score: -6.08563 Start: 65 End: 105 Full_Region: aattaaagaaggaag cggcataaaggcaa ttcccctaccccc ttgccgttttgccg ttttttttgtatctt ................................................................cggcataaaggcaattcccctacccccttgccgttttgccg......................... Find igs database================================================ Query_seq: TDE1175:TDE1176|TDE1175:TDE1176:chaperonin GroEL:oxygen-independent coproporphyrinogen III oxidase, putative:<-<-:1205242..1205371 130 tttagctctccttaagaatctatattaatttattaattatcgtgggtataagatacaaaaaaaacggcaaaacggcaagggggtaggggaattgcctttatgccgcttccttctttaattctttttgtta Intra-Species Hit: Count: 1 Min: 1 Max: 130 Len: 130 Subject: NC_002967_TDE1175_TDE1176|chaperonin GroEL:oxygen-independent coproporphyrinogen III oxidase, putative|NEGATIVE:NEGATIVE|[1205242,1205371]|130 HSP 1 e-value: 8.0E-54 bit: 210.0 Len: 130 Query Start:1 Query End:130 Subject Strand: POSITIVE Subject Start: 1 Subject End: 130 tttagctctccttaagaatctatattaatttattaattatcgtgggtataagatacnnnnnnnncggcaaaacggcaagggggtaggggaattgcctttatgccgcttccttctttaattctttttgtta tttagctctccttaagaatctatattaatttattaattatcgtgggtataagatacaaaaaaaacggcaaaacggcaagggggtaggggaattgcctttatgccgcttccttctttaattctttttgtta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAGCUCUCCUUAAGAAUCUAUAUUAAUUUAUUAAUUAUCGUGGGUAUAAGAUACAAAAAAAACGGCAAAACGGCAAGGGGGUAGGGGAAUUGCCUUUAUGCCGCUUCCUUCUUUAAUUCUUUUUGUUA ..........((((...((((((..(((((....)))))..)))))).)))).............((((((((((((..(((((((.....)))))))..))))).................))))))). (-24.52) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACAAAAAGAAUUAAAGAAGGAAGCGGCAUAAAGGCAAUUCCCCUACCCCCUUGCCGUUUUGCCGUUUUUUUUGUAUCUUAUACCCACGAUAAUUAAUAAAUUAAUAUAGAUUCUUAAGGAGAGCUAAA .......(((((((...(((((((((((((....(((((.............)))))....))))))))))))).((((..........)))).................)))))))............. (-27.42) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1026 110 61 201 152 NC_002967:TDE1175|5end_chaperonin_GroEL_1205151..1205381_NEGATIVE 422 110 65 70 25 NC_002967:TDE1974|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_1988910..1989140_NEGATIVE 419 105 63 66 20 NC_002967:TDE2618|5end_PHP_domain_protein_2659392..2659622_POSITIVE 375 114 74 218 177 NC_002967:TDE2516|5end_hypothetical_protein_2542021..2542251_POSITIVE 347 120 71 196 150 NC_002967:TDE1930|5end_hypothetical_protein_1948556..1948786_NEGATIVE 346 125 86 153 106 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 343 106 65 200 162 NC_002967:TDE1063|5end_methionyl-tRNA_synthetase_1090507..1090737_POSITIVE 335 109 64 46 6 NC_002967:TDE0239|5end_glycine_reductase_complex_protein_GrdD_272982..273212_NEGATIVE 330 109 63 73 26 NC_002967:TDE1547|5end_ribonuclease_HII_1591124..1591354_POSITIVE 329 114 72 225 187 NC_002967:TDE2762|5end_flagellar_motor_switch_protein_FliY_2817744..2817974_NEGATIVE 325 107 66 47 5 NC_002967:TDE0046|5end_formiminotransferase-cyclodeaminase_family_protein_55849..56079_NEGATIVE 323 105 63 62 26 NC_002967:TDE2715|5end_hypothetical_protein_2772668..2772898_POSITIVE 319 79 34 52 6 NC_002967:TDE1708|5end_apolipoprotein_N-acyltransferase_1764822..1765052_NEGATIVE 316 95 65 231 191 NC_002967:TDE0987|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1014041..1014271_POSITIVE 313 109 61 153 107 NC_002967:TDE0073|5end_riboflavin_biosynthesis_protein_RibF,_putative_84082..84312_NEGATIVE 305 110 65 55 4 NC_002967:TDE1886|5end_MiaB-like_tRNA_modifying_enzyme_1908488..1908718_NEGATIVE 301 110 61 53 9 NC_002967:TDE2323|5end_mechanosensitive_ion_channel_family_protein_2359084..2359314_NEGATIVE 301 120 73 171 116 NC_002967:TDE1669|5end_hemolysin_1722605..1722835_POSITIVE 301 109 64 67 29 NC_002967:TDE0885|5end_50S_ribosomal_protein_L19_902945..903175_POSITIVE 300 109 65 177 121 NC_002967:TDE0104|5end_3-dehydroquinate_synthase_124714..124944_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 347 118 73 84 13 NC_002967:TDE1131|3end_hypothetical_protein_1163531..1163681_POSITIVE 346 125 86 151 104 NC_002967:TDE0956|3end_hypothetical_protein_980330..980480_POSITIVE 335 109 65 53 2 NC_002967:TDE1980|3end_hypothetical_protein_1991960..1992110_NEGATIVE 334 110 63 69 18 NC_002967:TDE2729|3end_hypothetical_protein_2785756..2785906_NEGATIVE 330 109 63 73 26 NC_002967:TDE1546|3end_hypothetical_protein_1591204..1591354_POSITIVE 326 105 65 53 19 NC_002967:TDE1739|3end_femAB_family_protein_1792657..1792807_POSITIVE 326 109 65 33 2 NC_002967:TDE0240|3end_glycine_reductase_complex_protein_GrdC_272995..273145_NEGATIVE 324 97 55 151 109 NC_002967:TDE2292|3end_2C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase_2329383..2329533_POSITIVE 319 79 34 55 9 NC_002967:TDE1709|3end_DNA-binding_protein,_HU_family_1764819..1764969_NEGATIVE 318 119 71 114 63 NC_002967:TDE2719|3end_hypothetical_protein_2777015..2777165_POSITIVE 316 106 62 47 7 NC_002967:TDE0824|3end_lipoprotein,_putative_845226..845376_NEGATIVE 313 109 61 79 33 NC_002967:TDE0074|3end_amino_acid_permease_family_protein_84156..84306_NEGATIVE 307 104 62 83 34 NC_002967:TDE1913|3end_hypothetical_protein_1930897..1931047_POSITIVE 301 108 63 78 19 NC_002967:TDE0967|3end_hypothetical_protein_992529..992679_POSITIVE 301 109 64 74 36 NC_002967:TDE0884|3end_tRNA_(guanine-N(1)-)-methyltransferase_903032..903182_POSITIVE 296 116 74 98 54 NC_002967:TDE2293|3end_hypothetical_protein_2329325..2329475_NEGATIVE 296 110 65 148 103 NC_002967:TDE0105|3end_MTA/SAH_nucleosidase_124732..124882_NEGATIVE 294 109 62 129 65 NC_002967:TDE2310|3end_hypothetical_protein_2348256..2348406_POSITIVE 294 110 65 148 99 NC_002967:TDE0980|3end_asparaginyl-tRNA_synthetase_1003979..1004129_NEGATIVE 292 108 63 143 101 NC_002967:TDE2627|3end_transcriptional_regulator,_TetR_family_2668532..2668682_NEGATIVE