Origin IGS: cttaccctccaattatattacttagtaatattactaagtaatataatactctttctcggcacacttgtcaagccgatattgcataattttttatatagacatattgaatattttgataaaattatgataagattatgatatgagagtttttattggaggtgtca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgacacctccaataaaaactctcatatcataatcttatcataattttatcaaaatattcaatatgtctatataaaaaattatgcaatatcggcttgacaagtgtgccgagaaagagtattatattacttagtaatattactaagtaatataattggagggtaag Mask Tandem Repeat Region ================================================ cttaccctccaattnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaatactctttctcggcacacttgtcaagccgatattgcataattttttatatagacatattgaatattttgataaaattatgataagattatgatatgagagtttttattggaggtgtca Find is-nt database================================================ Query_seq: TDE1953:TDE1954|TDE1953:TDE1954:transcriptional regulator, TetR family:prevent-host-death family protein:<-->:1969762..1969925 164 cttaccctccaattatattacttagtaatattactaagtaatataatactctttctcggcacacttgtcaagccgatattgcataattttttatatagacatattgaatattttgataaaattatgataagattatgatatgagagtttttattggaggtgtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1953:TDE1954|TDE1953:TDE1954:transcriptional regulator, TetR family:prevent-host-death family protein:<-->:1969762..1969925 164 cttaccctccaattatattacttagtaatattactaagtaatataatactctttctcggcacacttgtcaagccgatattgcataattttttatatagacatattgaatattttgataaaattatgataagattatgatatgagagtttttattggaggtgtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1953:TDE1954|TDE1953:TDE1954:transcriptional regulator, TetR family:prevent-host-death family protein:<-->:1969762..1969925 164 cttaccctccaattatattacttagtaatattactaagtaatataatactctttctcggcacacttgtcaagccgatattgcataattttttatatagacatattgaatattttgataaaattatgataagattatgatatgagagtttttattggaggtgtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttaccctccaattatattacttagtaatattactaagtaatataatactctttctcggcacacttgtcaagccgatattgcataattttttatatagacatattgaatattttgataaaattatgataagattatgatatgagagtttttattggaggtgtca Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 28 End: 135 ........................... M L L S N I I L F L G T L V K P I L H N F L Y R H I E Y F D K I M I R L ............................. Protein_Len: 36 Strand: - Start: 21 End: 128 .................... K T I N S L L I I S K R P V S T L G I N C L K K Y L C I S Y K S L I I M .................................... cttaccctccaattatattacttagtaatattactaagtaatataatactctttctcggcacacttgtcaagccgatattgcataattttttatatagacatattgaatattttgataaaattatgataagattatgatatgagagtttttattggaggtgtca 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: 88 Start: 43 End: 72 ..........................................CTTGACAAGTGTGCCGAGAAAGAGTATTAT............................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttaccctccaattatattacttagtaatattactaagtaatataatactctttctcggcacacttgtcaagccgatattgcataattttttatatagacatattgaatattttgataaaattatgataagattatgatatgagagtttttattggaggtgtca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 80 HP_score: -9.8 Tail_Score: -2.90392 Start: 18 End: 41 Full_Region: agaaagagtattata ttacttagta atat tactaagtaa tataattggagggta .................ttacttagtaatattactaagtaa........................................................................................................................... Find igs database================================================ Query_seq: TDE1953:TDE1954|TDE1953:TDE1954:transcriptional regulator, TetR family:prevent-host-death family protein:<-->:1969762..1969925 164 cttaccctccaattatattacttagtaatattactaagtaatataatactctttctcggcacacttgtcaagccgatattgcataattttttatatagacatattgaatattttgataaaattatgataagattatgatatgagagtttttattggaggtgtca Intra-Species Hit: Count: 1 Min: 1 Max: 164 Len: 164 Subject: NC_002967_TDE1953_TDE1954|transcriptional regulator, TetR family:prevent-host-death family protein|NEGATIVE:POSITIVE|[1969762,1969925]|164 HSP 1 e-value: 3.0E-88 bit: 325.0 Len: 164 Query Start:1 Query End:164 Subject Strand: POSITIVE Subject Start: 1 Subject End: 164 cttaccctccaattatattacttagtaatattactaagtaatataatactctttctcggcacacttgtcaagccgatattgcataattttttatatagacatattgaatattttgataaaattatgataagattatgatatgagagtttttattggaggtgtca cttaccctccaattatattacttagtaatattactaagtaatataatactctttctcggcacacttgtcaagccgatattgcataattttttatatagacatattgaatattttgataaaattatgataagattatgatatgagagtttttattggaggtgtca HSP 2 e-value: 6.0E-12 bit: 71.9 Len: 36 Query Start:12 Query End:47 Subject Strand: NEGATIVE Subject Start: 12 Subject End: 47 ...........attatattacttagtaatattactaagtaatataat..................................................................................................................... ...........attatattacttagtaatattactaagtaatataat..................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUACCCUCCAAUUAUAUUACUUAGUAAUAUUACUAAGUAAUAUAAUACUCUUUCUCGGCACACUUGUCAAGCCGAUAUUGCAUAAUUUUUUAUAUAGACAUAUUGAAUAUUUUGAUAAAAUUAUGAUAAGAUUAUGAUAUGAGAGUUUUUAUUGGAGGUGUCA ...((((((((((((((((((((((((....))))))))))))))..((((((..(((((...........))))).....((((((((((((((......(((..(.....)..)))....))))).)))))))))....))))))....)))))))).)).. (-45.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGACACCUCCAAUAAAAACUCUCAUAUCAUAAUCUUAUCAUAAUUUUAUCAAAAUAUUCAAUAUGUCUAUAUAAAAAAUUAUGCAAUAUCGGCUUGACAAGUGUGCCGAGAAAGAGUAUUAUAUUACUUAGUAAUAUUACUAAGUAAUAUAAUUGGAGGGUAAG ..((.((((((((....(((((................(((((((((......((((.....))))........))))))))).....(((((...........)))))...)))))..((((((((((((((....))))))))))))))))))))))))... (-41.84) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 827 100 51 191 142 NC_002967:TDE1953|5end_transcriptional_regulator,_TetR_family_1969671..1969901_NEGATIVE 269 76 49 164 127 NC_002967:TDE2347|5end_30S_ribosomal_protein_S2_2384378..2384608_NEGATIVE 268 81 50 226 188 NC_002967:TDE2197|5end_hypothetical_protein_2232848..2233078_NEGATIVE 241 89 45 177 122 NC_002967:TDE0988|5end_oligopeptide/dipeptide_ABC_transporter,_peptide-binding_protein_1015082..1015312_POSITIVE 241 82 44 45 5 NC_002967:TDE0740|5end_hypothetical_protein_775987..776217_POSITIVE 239 85 49 71 37 NC_002967:TDE2770|5end_flagellar_hook-length_control_protein_FliK_2824417..2824647_NEGATIVE 239 77 48 141 108 NC_002967:TDE2160|5end_hypothetical_protein_2193968..2194198_NEGATIVE 239 89 49 202 160 NC_002967:TDE0314|5end_hypothetical_protein_346077..346307_POSITIVE 237 84 53 166 137 NC_002967:TDE0797|5end_acylphosphatase_820859..821089_POSITIVE 236 74 36 175 120 NC_002967:TDE0455|5end_kinase,_GHMP_family_511192..511422_POSITIVE 234 94 53 76 33 NC_002967:TDE2504|5end_O-sialoglycoprotein_endopeptidase_2529001..2529231_POSITIVE 231 83 57 110 82 NC_002967:TDE2516|5end_hypothetical_protein_2542021..2542251_POSITIVE 230 92 56 190 161 NC_002967:TDE0410|5end_peptidase,_M48_family_462053..462283_POSITIVE 226 76 49 34 8 NC_002967:TDE0305|5end_GTP-binding_protein_YchF_336751..336981_NEGATIVE 225 82 55 152 121 NC_002967:TDE2479|5end_hypothetical_protein_2503290..2503520_NEGATIVE 225 94 57 31 1 NC_002967:TDE1501|5end_pyruvate_phosphate_dikinase_1548041..1548271_POSITIVE 224 82 45 125 79 NC_002967:TDE2465|5end_hypothetical_protein_2489651..2489881_NEGATIVE 224 76 52 167 145 NC_002967:TDE1975|5end_hypothetical_protein_1988869..1989099_POSITIVE 224 83 42 141 92 NC_002967:TDE1624|5end_glycine_dehydrogenase_subunit_2_1673519..1673749_NEGATIVE 222 86 49 61 25 NC_002967:TDE0169|5end_methyl-accepting_chemotaxis_domain_protein_198792..199022_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 84 49 52 21 NC_002967:TDE2196|3end_hypothetical_protein_2231883..2232033_NEGATIVE 241 89 45 92 37 NC_002967:TDE0987|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1015077..1015227_POSITIVE 238 74 45 53 20 NC_002967:TDE2460|3end_aminotransferase,_class_V_2487229..2487379_POSITIVE 234 94 53 74 31 NC_002967:TDE2503|3end_hypothetical_protein_2529079..2529229_POSITIVE 230 77 31 129 84 NC_002967:TDE1278|3end_conserved_hypothetical_protein_TIGR01440_1312228..1312378_NEGATIVE 227 76 49 107 71 NC_002967:TDE2219|3end_hypothetical_protein_2258961..2259111_NEGATIVE 225 82 55 76 45 NC_002967:TDE2480|3end_heat_shock_protein_90_2503366..2503516_NEGATIVE 224 82 45 125 79 NC_002967:TDE2466|3end_hypothetical_protein_2489651..2489801_NEGATIVE 224 83 42 141 92 NC_002967:TDE1625|3end_glycine_cleavage_system_P_protein,_subunit_1_1673519..1673669_NEGATIVE 222 83 47 35 2 NC_002967:TDE1396|3end_hypothetical_protein_1436127..1436277_POSITIVE 221 82 48 149 111 NC_002967:TDE0842|3end_cytoplasmic_filament_protein_A_863843..863993_POSITIVE 221 101 65 109 72 NC_002967:TDE0840|3end_hypothetical_protein_859419..859569_NEGATIVE 220 83 54 52 14 NC_002967:TDE0394|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_445023..445173_POSITIVE 219 82 52 44 18 NC_002967:TDE0845|3end_conserved_hypothetical_protein_TIGR00266_868549..868699_POSITIVE 218 74 34 105 62 NC_002967:TDE1632|3end_citrate_lyase,_beta_subunit_1681569..1681719_NEGATIVE 218 83 55 56 30 NC_002967:TDE1469|3end_conserved_hypothetical_protein_TIGR00150_1517333..1517483_NEGATIVE 214 90 49 141 106 NC_002967:TDE2312|3end_hypothetical_protein_2349049..2349199_POSITIVE 214 95 56 151 116 NC_002967:TDE2053|3end_NifU_domain_protein_2082153..2082303_POSITIVE 214 75 52 149 121 NC_002967:TDE0994|3end_hypothetical_protein_1022447..1022597_POSITIVE 213 76 46 42 14 NC_002967:TDE0602|3end_3-oxoacyl-(acyl-carrier-protein)_synthase_III_639836..639986_NEGATIVE