Origin IGS: tttttctgagattctccaataatttgatatacgtttgacattagctaacattgtataataatttaggaaaaaaagcaatatttttattttttttgttgacagccatttaaaaccgtgttatacttttcttaaagtgaacatgttcactatgcattataggaatgtgattgttttaagatttttttatgagtaggtggctta .........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 taagccacctactcataaaaaaatcttaaaacaatcacattcctataatgcatagtgaacatgttcactttaagaaaagtataacacggttttaaatggctgtcaacaaaaaaaataaaaatattgctttttttcctaaattattatacaatgttagctaatgtcaaacgtatatcaaattattggagaatctcagaaaaa Mask Tandem Repeat Region ================================================ tttttctgagattctccaataatttgatatacgtttgacattagctaacattgtataataatttaggaaaaaaagcaatatttttattttttttgttgacagccatttaaaaccgtgttatacttttcttaaagtgaacatgttcactatgcattataggaatgtgattgttttaagatttttttatgagtaggtggctta Find is-nt database================================================ Query_seq: TDE0393:TDE0394|TDE0393:TDE0394:transcriptional regulator, TetR family:oligopeptide/dipeptide ABC transporter, permease protein:<-->:443920..444120 201 tttttctgagattctccaataatttgatatacgtttgacattagctaacattgtataataatttaggaaaaaaagcaatatttttattttttttgttgacagccatttaaaaccgtgttatacttttcttaaagtgaacatgttcactatgcattataggaatgtgattgttttaagatttttttatgagtaggtggctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0393:TDE0394|TDE0393:TDE0394:transcriptional regulator, TetR family:oligopeptide/dipeptide ABC transporter, permease protein:<-->:443920..444120 201 tttttctgagattctccaataatttgatatacgtttgacattagctaacattgtataataatttaggaaaaaaagcaatatttttattttttttgttgacagccatttaaaaccgtgttatacttttcttaaagtgaacatgttcactatgcattataggaatgtgattgttttaagatttttttatgagtaggtggctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0393:TDE0394|TDE0393:TDE0394:transcriptional regulator, TetR family:oligopeptide/dipeptide ABC transporter, permease protein:<-->:443920..444120 201 tttttctgagattctccaataatttgatatacgtttgacattagctaacattgtataataatttaggaaaaaaagcaatatttttattttttttgttgacagccatttaaaaccgtgttatacttttcttaaagtgaacatgttcactatgcattataggaatgtgattgttttaagatttttttatgagtaggtggctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttttctgagattctccaataatttgatatacgtttgacattagctaacattgtataataatttaggaaaaaaagcaatatttttattttttttgttgacagccatttaaaaccgtgttatacttttcttaaagtgaacatgttcactatgcattataggaatgtgattgttttaagatttttttatgagtaggtggctta Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 80 End: 190 ............................................................................... M F I F F V D S H L K P C Y T F L K V N M F T M H Y R N V I V L R F F Y E ........... Protein_Len: 34 Strand: - Start: 1 End: 102 K E S I R W Y N S I R K V N A L M T Y Y N L F F L L I K I K K T S M ................................................................................................... tttttctgagattctccaataatttgatatacgtttgacattagctaacattgtataataatttaggaaaaaaagcaatatttttattttttttgttgacagccatttaaaaccgtgttatacttttcttaaagtgaacatgttcactatgcattataggaatgtgattgttttaagatttttttatgagtaggtggctta 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: 95 End: 124 ..............................................................................................GTTGACAGCCATTTAAAACCGTGTTATACT............................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 50 End: 79 .................................................ATTGCTTTTTTTCCTAAATTATTATACAAT.......................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttttctgagattctccaataatttgatatacgtttgacattagctaacattgtataataatttaggaaaaaaagcaatatttttattttttttgttgacagccatttaaaaccgtgttatacttttcttaaagtgaacatgttcactatgcattataggaatgtgattgttttaagatttttttatgagtaggtggctta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -2.6 Tail_Score: -5.64274 Start: 127 End: 178 Full_Region: ACCGTGTTATACTTT TCTTAAAGTGAACATGTTCACTATG CAT TATAGGAATGTGATTGTTTTAAGA TTTTTTTATGAGTAG ..............................................................................................................................TCTTAAAGTGAACATGTTCACTATGCATTATAGGAATGTGATTGTTTTAAGA....................... Find igs database================================================ Query_seq: TDE0393:TDE0394|TDE0393:TDE0394:transcriptional regulator, TetR family:oligopeptide/dipeptide ABC transporter, permease protein:<-->:443920..444120 201 tttttctgagattctccaataatttgatatacgtttgacattagctaacattgtataataatttaggaaaaaaagcaatatttttattttttttgttgacagccatttaaaaccgtgttatacttttcttaaagtgaacatgttcactatgcattataggaatgtgattgttttaagatttttttatgagtaggtggctta Intra-Species Hit: Count: 1 Min: 1 Max: 201 Len: 201 Subject: NC_002967_TDE0393_TDE0394|transcriptional regulator, TetR family:oligopeptide/dipeptide ABC transporter, permease protein|NEGATIVE:POSITIVE|[443920,444120]|201 HSP 1 e-value: 1.0E-41 bit: 170.0 Len: 107 Query Start:95 Query End:201 Subject Strand: POSITIVE Subject Start: 95 Subject End: 201 ..............................................................................................gttgacagccatttaaaaccgtgttatacttttcttaaagtgaacatgttcactatgcattataggaatgtgattgttttaagannnnnnnatgagtaggtggctta ..............................................................................................gttgacagccatttaaaaccgtgttatacttttcttaaagtgaacatgttcactatgcattataggaatgtgattgttttaagatttttttatgagtaggtggctta HSP 2 e-value: 2.0E-30 bit: 133.0 Len: 67 Query Start:1 Query End:67 Subject Strand: POSITIVE Subject Start: 1 Subject End: 67 tttttctgagattctccaataatttgatatacgtttgacattagctaacattgtataataatttagg...................................................................................................................................... tttttctgagattctccaataatttgatatacgtttgacattagctaacattgtataataatttagg...................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUCUGAGAUUCUCCAAUAAUUUGAUAUACGUUUGACAUUAGCUAACAUUGUAUAAUAAUUUAGGAAAAAAAGCAAUAUUUUUAUUUUUUUUGUUGACAGCCAUUUAAAACCGUGUUAUACUUUUCUUAAAGUGAACAUGUUCACUAUGCAUUAUAGGAAUGUGAUUGUUUUAAGAUUUUUUUAUGAGUAGGUGGCUUA ((((((((((......(((....))).((((((..................))))))....))))))))))....(((((.............)))))..(((((((((....((((.........((((((((..(.(((((((.(((((...)))))))))))).)..))))))))......))))..))))))))).. (-37.85) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCCACCUACUCAUAAAAAAAUCUUAAAACAAUCACAUUCCUAUAAUGCAUAGUGAACAUGUUCACUUUAAGAAAAGUAUAACACGGUUUUAAAUGGCUGUCAACAAAAAAAAUAAAAAUAUUGCUUUUUUUCCUAAAUUAUUAUACAAUGUUAGCUAAUGUCAAACGUAUAUCAAAUUAUUGGAGAAUCUCAGAAAAA .((((..................((((((........((((.....))))...((((((....))))))))))))..........((((((......))))))......................)))).((((((..((((..(((((....((..(....)..))..)))))...))))...))))))........... (-22.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 746 140 91 231 182 NC_002967:TDE0393|5end_transcriptional_regulator,_TetR_family_443829..444059_NEGATIVE 295 130 81 208 164 NC_002967:TDE1299|5end_hypothetical_protein_1336613..1336843_NEGATIVE 249 200 151 185 134 NC_002967:TDE0066|5end_hypothetical_protein_73926..74156_NEGATIVE 231 199 156 223 182 NC_002967:TDE1748|5end_GTP-binding_protein,_GTP1/Obg_family_1803080..1803310_NEGATIVE 227 119 74 50 2 NC_002967:TDE2725|5end_cyclic_nucleotide_binding_domain/GGDEF_domain_protein_2783208..2783438_NEGATIVE 223 160 114 170 115 NC_002967:TDE1023|5end_methylaspartate_mutase_subunit_S_1055123..1055353_POSITIVE 222 46 4 170 124 NC_002967:TDE0330|5end_CRISPR-associated_SAG0897_family_protein_366244..366474_POSITIVE 221 168 125 225 189 NC_002967:TDE0396|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_445812..446042_POSITIVE 216 130 100 182 150 NC_002967:TDE2197|5end_hypothetical_protein_2232848..2233078_NEGATIVE 215 199 155 139 99 NC_002967:TDE1741|5end_penicillin-binding_protein_1792792..1793022_POSITIVE 213 174 139 129 83 NC_002967:TDE1565|5end_hypothetical_protein_1616893..1617123_POSITIVE 211 170 123 198 151 NC_002967:TDE0956|5end_hypothetical_protein_979456..979686_POSITIVE 210 157 112 97 44 NC_002967:TDE0774|5end_50S_ribosomal_protein_L16_810165..810395_POSITIVE 210 127 83 223 184 NC_002967:TDE0081|5end_hypothetical_protein_93941..94171_NEGATIVE 206 118 81 135 101 NC_002967:TDE1420|5end_hypothetical_protein_1464375..1464605_POSITIVE 202 130 90 71 33 NC_002967:TDE2303|5end_hypothetical_protein_2343055..2343285_POSITIVE 201 198 167 102 77 NC_002967:TDE0577|5end_glutamyl-tRNA(Gln)_amidotransferase,_C_subunit_609509..609739_NEGATIVE 199 154 114 128 89 NC_002967:TDE0718|5end_hypothetical_protein_753215..753445_POSITIVE 198 48 1 219 178 NC_002967:TDE0036|5end_hypothetical_protein_42527..42757_NEGATIVE 197 104 74 221 190 NC_002967:TDE1003|5end_hypothetical_protein_1029111..1029341_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 252 200 157 150 103 NC_002967:TDE1494|3end_chemotaxis_protein_CheY_1539596..1539746_POSITIVE 243 130 82 118 59 NC_002967:TDE2299|3end_apolipoprotein_N-acyltransferase_2339937..2340087_POSITIVE 231 199 156 145 104 NC_002967:TDE1749|3end_50S_ribosomal_protein_L27_1803158..1803308_NEGATIVE 227 119 74 57 9 NC_002967:TDE2726|3end_cyclic_nucleotide_binding_domain/GGDEF_domain_protein_2783201..2783351_NEGATIVE 216 130 100 128 96 NC_002967:TDE2198|3end_pyruvate-ferredoxin_oxidoreductase_2232902..2233052_NEGATIVE 210 157 112 94 41 NC_002967:TDE0773|3end_30S_ribosomal_protein_S3_810242..810392_POSITIVE 206 118 81 133 99 NC_002967:TDE1419|3end_glycosyl_transferase,_group_2_family_protein_1464453..1464603_POSITIVE 202 130 90 71 33 NC_002967:TDE2302|3end_HD_domain_protein_2343135..2343285_POSITIVE 196 200 168 92 47 NC_002967:TDE1380|3end_hypothetical_protein_1420733..1420883_NEGATIVE 194 50 1 141 94 NC_002967:TDE1736|3end_ferredoxin,_2(4Fe-4S)_1790158..1790308_POSITIVE 194 159 111 72 25 NC_002967:TDE0785|3end_ribosomal_protein_L30_814682..814832_POSITIVE 193 132 91 73 35 NC_002967:TDE2084|3end_RNA_methyltransferase,_TrmH_family_2114229..2114379_POSITIVE 193 146 101 78 33 NC_002967:TDE1397|3end_flagellar_synthesis_regulator_FleN,_putative_1437260..1437410_POSITIVE 193 136 92 144 100 NC_002967:TDE0011|3end_alkyl_hydroperoxide_reductase/peroxiredoxin_16135..16285_POSITIVE 192 197 152 145 89 NC_002967:TDE2473|3end_30S_ribosomal_protein_S21_2496587..2496737_POSITIVE 191 23 4 150 127 NC_002967:TDE0329|3end_CRISPR-associated_protein_Cas2_366327..366477_POSITIVE 191 165 127 137 89 NC_002967:TDE0269|3end_hypothetical_protein_300196..300346_NEGATIVE 190 165 124 91 56 NC_002967:TDE2201|3end_hypothetical_protein_2238492..2238642_NEGATIVE 189 45 6 138 107 NC_002967:TDE2120|3end_glycine_reductase_complex_proprotein_GrdE2_2152705..2152855_NEGATIVE 187 160 113 131 84 NC_002967:TDE1140|3end_hypothetical_protein_1168730..1168880_NEGATIVE