Origin IGS: agatttttaactgcaagcggctcaaggaatgtgcagtttggtttaaaaatttcttataaggtgatttaagggagtttataaaagcatcagtttttatgggctcccttaaatattatcggttctcgaaacacctctttatgtggataggatccataaaaatcaacatagttttataaatttaatctttcggcttgacataaataaaattatatggtaaattatgaatgaataattataaatattcattcataaagaggttgaa .........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 ttcaacctctttatgaatgaatatttataattattcattcataatttaccatataattttatttatgtcaagccgaaagattaaatttataaaactatgttgatttttatggatcctatccacataaagaggtgtttcgagaaccgataatatttaagggagcccataaaaactgatgcttttataaactcccttaaatcaccttataagaaatttttaaaccaaactgcacattccttgagccgcttgcagttaaaaatct Mask Tandem Repeat Region ================================================ agatttttaactgcaagcggctcaaggaatgtgcagtttggtttaaaaatttcttataaggtgatttaagggagtttataaaagcatcagtttttatgggctcccttaaatattatcggttctcgaaacacctctttatgtggataggatccataaaaatcaacatagttttataaatttaatctttcggcttgacataaataaaattatatggtaaattatgaatgaataattataaatattcattcataaagaggttgaa Find is-nt database================================================ Query_seq: TDE1364:TDE1365|TDE1364:TDE1365:valyl-tRNA synthetase:transcriptional regulator, TetR family:->->:1407633..1407894 262 agatttttaactgcaagcggctcaaggaatgtgcagtttggtttaaaaatttcttataaggtgatttaagggagtttataaaagcatcagtttttatgggctcccttaaatattatcggttctcgaaacacctctttatgtggataggatccataaaaatcaacatagttttataaatttaatctttcggcttgacataaataaaattatatggtaaattatgaatgaataattataaatattcattcataaagaggttgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1364:TDE1365|TDE1364:TDE1365:valyl-tRNA synthetase:transcriptional regulator, TetR family:->->:1407633..1407894 262 agatttttaactgcaagcggctcaaggaatgtgcagtttggtttaaaaatttcttataaggtgatttaagggagtttataaaagcatcagtttttatgggctcccttaaatattatcggttctcgaaacacctctttatgtggataggatccataaaaatcaacatagttttataaatttaatctttcggcttgacataaataaaattatatggtaaattatgaatgaataattataaatattcattcataaagaggttgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1364:TDE1365|TDE1364:TDE1365:valyl-tRNA synthetase:transcriptional regulator, TetR family:->->:1407633..1407894 262 agatttttaactgcaagcggctcaaggaatgtgcagtttggtttaaaaatttcttataaggtgatttaagggagtttataaaagcatcagtttttatgggctcccttaaatattatcggttctcgaaacacctctttatgtggataggatccataaaaatcaacatagttttataaatttaatctttcggcttgacataaataaaattatatggtaaattatgaatgaataattataaatattcattcataaagaggttgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agatttttaactgcaagcggctcaaggaatgtgcagtttggtttaaaaatttcttataaggtgatttaagggagtttataaaagcatcagtttttatgggctcccttaaatattatcggttctcgaaacacctctttatgtggataggatccataaaaatcaacatagttttataaatttaatctttcggcttgacataaataaaattatatggtaaattatgaatgaataattataaatattcattcataaagaggttgaa Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 78 End: 173 ............................................................................. M K A S V F M G S L K Y Y R F S K H L F M W I G S I K I N I V L ......................................................................................... Protein_Len: 35 Strand: + Start: 110 End: 214 ............................................................................................................. M L S V L E T P L Y V D R I H K N Q H S F I N L I F R L D I N K I I W ................................................ Protein_Len: 32 Strand: - Start: 2 End: 97 . I K L Q L R S L S H A T Q N L F K K Y P S K L S N I F A D T K M ..................................................................................................................................................................... agatttttaactgcaagcggctcaaggaatgtgcagtttggtttaaaaatttcttataaggtgatttaagggagtttataaaagcatcagtttttatgggctcccttaaatattatcggttctcgaaacacctctttatgtggataggatccataaaaatcaacatagttttataaatttaatctttcggcttgacataaataaaattatatggtaaattatgaatgaataattataaatattcattcataaagaggttgaa 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: 87 Start: 191 End: 220 ..............................................................................................................................................................................................CTTGACATAAATAAAATTATATGGTAAATT.......................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agatttttaactgcaagcggctcaaggaatgtgcagtttggtttaaaaatttcttataaggtgatttaagggagtttataaaagcatcagtttttatgggctcccttaaatattatcggttctcgaaacacctctttatgtggataggatccataaaaatcaacatagttttataaatttaatctttcggcttgacataaataaaattatatggtaaattatgaatgaataattataaatattcattcataaagaggttgaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 95 HP_score: -12.5 Tail_Score: -3.45054 Start: 63 End: 112 Full_Region: AATTTCTTATAAGGT GATTTAAGGGAGTTTATAAAAGC ATCA GTTTTTATGGGCTCCCTTAAATA TTATCGGTTCTCGAA ..............................................................GATTTAAGGGAGTTTATAAAAGCATCAGTTTTTATGGGCTCCCTTAAATA...................................................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -15.1 Tail_Score: -3.29558 Start: 65 End: 110 Full_Region: TTTCTTATAAGGTGA TTTAAGGGAGTTTATAAAAGC ATCA GTTTTTATGGGCTCCCTTAAA TATTATCGGTTCTCG ................................................................TTTAAGGGAGTTTATAAAAGCATCAGTTTTTATGGGCTCCCTTAAA........................................................................................................................................................ Find igs database================================================ Query_seq: TDE1364:TDE1365|TDE1364:TDE1365:valyl-tRNA synthetase:transcriptional regulator, TetR family:->->:1407633..1407894 262 agatttttaactgcaagcggctcaaggaatgtgcagtttggtttaaaaatttcttataaggtgatttaagggagtttataaaagcatcagtttttatgggctcccttaaatattatcggttctcgaaacacctctttatgtggataggatccataaaaatcaacatagttttataaatttaatctttcggcttgacataaataaaattatatggtaaattatgaatgaataattataaatattcattcataaagaggttgaa Intra-Species Hit: Count: 1 Min: 1 Max: 262 Len: 262 Subject: NC_002967_TDE1364_TDE1365|valyl-tRNA synthetase:transcriptional regulator, TetR family|POSITIVE:POSITIVE|[1407633,1407894]|262 HSP 1 e-value: 1.0E-146 bit: 519.0 Len: 262 Query Start:1 Query End:262 Subject Strand: POSITIVE Subject Start: 1 Subject End: 262 agatttttaactgcaagcggctcaaggaatgtgcagtttggtttaaaaatttcttataaggtgatttaagggagtttataaaagcatcagtttttatgggctcccttaaatattatcggttctcgaaacacctctttatgtggataggatccataaaaatcaacatagttttataaatttaatctttcggcttgacataaataaaattatatggtaaattatgaatgaataattataaatattcattcataaagaggttgaa agatttttaactgcaagcggctcaaggaatgtgcagtttggtttaaaaatttcttataaggtgatttaagggagtttataaaagcatcagtttttatgggctcccttaaatattatcggttctcgaaacacctctttatgtggataggatccataaaaatcaacatagttttataaatttaatctttcggcttgacataaataaaattatatggtaaattatgaatgaataattataaatattcattcataaagaggttgaa HSP 2 e-value: 1.0E-5 bit: 52.0 Len: 34 Query Start:219 Query End:252 Subject Strand: NEGATIVE Subject Start: 219 Subject End: 252 ..........................................................................................................................................................................................................................ttatgaatgaataattataaatattcattcataa.......... ..........................................................................................................................................................................................................................ttatgaatgaatatttataattattcattcataa.......... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAUUUUUAACUGCAAGCGGCUCAAGGAAUGUGCAGUUUGGUUUAAAAAUUUCUUAUAAGGUGAUUUAAGGGAGUUUAUAAAAGCAUCAGUUUUUAUGGGCUCCCUUAAAUAUUAUCGGUUCUCGAAACACCUCUUUAUGUGGAUAGGAUCCAUAAAAAUCAACAUAGUUUUAUAAAUUUAAUCUUUCGGCUUGACAUAAAUAAAAUUAUAUGGUAAAUUAUGAAUGAAUAAUUAUAAAUAUUCAUUCAUAAAGAGGUUGAA ((((((((((...(((((.((.((.....)).)).)))))..))))))))))......(((((((((((((((((((((((((((....))))))))))))))))))))))....(((.....)))..))))).....(((((((...)))))))....(((((.(((((((((....((((.(.....).)))).....))))))))).........(((((((((((((........)))))))))))))....))))). (-71.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCAACCUCUUUAUGAAUGAAUAUUUAUAAUUAUUCAUUCAUAAUUUACCAUAUAAUUUUAUUUAUGUCAAGCCGAAAGAUUAAAUUUAUAAAACUAUGUUGAUUUUUAUGGAUCCUAUCCACAUAAAGAGGUGUUUCGAGAACCGAUAAUAUUUAAGGGAGCCCAUAAAAACUGAUGCUUUUAUAAACUCCCUUAAAUCACCUUAUAAGAAAUUUUUAAACCAAACUGCACAUUCCUUGAGCCGCUUGCAGUUAAAAAUCU .(((((....(((((((((((((........))))))))))))).......(((((.((((.((...((.....))..)).)))).))))).......)))))......(((((...)))))......((((((..(((.....)))....(((((((((((...((((((.(....).))))))...))))))))))))))))).......((((((((..(((.(.((.((.....)).)).).)))...)))))))).. (-54.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 417 119 71 166 117 NC_002967:TDE2256|5end_hypothetical_protein_2293387..2293617_NEGATIVE 304 44 12 42 8 NC_002967:TDE1970|5end_sensory_box_histidine_kinase_1985744..1985974_NEGATIVE 296 108 61 153 103 NC_002967:TDE2219|5end_hypothetical_protein_2260646..2260876_NEGATIVE 278 135 98 186 154 NC_002967:TDE0252|5end_hypothetical_protein_286263..286493_POSITIVE 277 108 69 157 111 NC_002967:TDE2461|5end_selenide,_water_dikinase_(selenocysteine-containing)_2488260..2488490_NEGATIVE 272 43 12 221 187 NC_002967:TDE1001|5end_orotate_phosphoribosyltransferase_1027653..1027883_POSITIVE 271 43 3 56 20 NC_002967:TDE0499|5end_hypothetical_protein_553497..553727_NEGATIVE 268 50 9 148 108 NC_002967:TDE2480|5end_heat_shock_protein_90_2505288..2505518_NEGATIVE 260 53 12 226 184 NC_002967:TDE1597|5end_transporter,_putative_1647402..1647632_NEGATIVE 255 103 61 64 29 NC_002967:TDE2245|5end_DNA_topoisomerase_IV_subunit_B_2284240..2284470_POSITIVE 251 148 101 207 146 NC_002967:TDE1135|5end_hypothetical_protein_1165542..1165772_NEGATIVE 250 44 8 158 126 NC_002967:TDE2745|5end_fic_family_protein_2800696..2800926_NEGATIVE 249 148 111 199 145 NC_002967:TDE0561|5end_hypothetical_protein_594245..594475_POSITIVE 249 148 111 116 62 NC_002967:TDE0560|5end_hypothetical_protein_594162..594392_POSITIVE 248 102 62 178 131 NC_002967:TDE1034|5end_magnesium_and_cobalt_transporter,_putative_1062454..1062684_POSITIVE 247 104 70 225 183 NC_002967:TDE2276|5end_hypothetical_protein_2312676..2312906_NEGATIVE 246 40 5 162 118 NC_002967:TDE2522|5end_ABC_transporter,_ATP-binding_protein_2548098..2548328_POSITIVE 244 104 71 108 75 NC_002967:TDE0629|5end_chaperone_protein_DnaJ_662587..662817_POSITIVE 243 42 1 138 93 NC_002967:TDE2355|5end_carbon_storage_regulator_2390838..2391068_POSITIVE 243 124 84 73 39 NC_002967:TDE0574|5end_surface_protein,_putative_604925..605155_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 417 119 71 50 1 NC_002967:TDE2257|3end_5'-nucleotidase_family_protein_2293503..2293653_NEGATIVE 315 107 61 90 42 NC_002967:TDE1264|3end_hypothetical_protein_1298152..1298302_NEGATIVE 304 44 12 45 11 NC_002967:TDE1971|3end_DNA_polymerase_III_domain_protein_1985741..1985891_NEGATIVE 290 123 82 150 102 NC_002967:TDE2374|3end_precorrin-8W_decarboxylase,_putative_2406352..2406502_POSITIVE 277 108 69 112 66 NC_002967:TDE2462|3end_hypothetical_protein_2488305..2488455_NEGATIVE 269 44 2 63 4 NC_002967:TDE0973|3end_DNA_repair_protein_RadC_997940..998090_NEGATIVE 268 50 9 84 44 NC_002967:TDE2481|3end_hypothetical_protein_2505352..2505502_NEGATIVE 264 107 61 76 26 NC_002967:TDE0399|3end_zinc_carboxypeptidase_family_protein_450845..450995_POSITIVE 259 54 12 112 73 NC_002967:TDE1451|3end_hypothetical_protein_1497850..1498000_NEGATIVE 256 57 11 51 8 NC_002967:TDE1278|3end_conserved_hypothetical_protein_TIGR01440_1312228..1312378_NEGATIVE 255 103 61 64 29 NC_002967:TDE2244|3end_hypothetical_protein_2284320..2284470_POSITIVE 254 42 1 82 40 NC_002967:TDE2268|3end_hypothetical_protein_2304822..2304972_NEGATIVE 248 102 62 139 92 NC_002967:TDE1033|3end_polyA_polymerase_family_protein_1062495..1062645_POSITIVE 248 108 69 87 47 NC_002967:TDE0185|3end_ABC_transporter,_ATP-binding_protein,_HlyB_family_222335..222485_POSITIVE 244 104 71 70 37 NC_002967:TDE0628|3end_molecular_chaperone_DnaK_662629..662779_POSITIVE 243 42 1 138 93 NC_002967:TDE2354|3end_hypothetical_protein_2390918..2391068_POSITIVE 241 55 11 107 35 NC_002967:TDE0268|3end_hypothetical_protein_299219..299369_NEGATIVE 240 44 2 90 39 NC_002967:TDE0135|3end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_156377..156527_POSITIVE 238 137 97 114 74 NC_002967:TDE1344|3end_hypothetical_protein_1383350..1383500_POSITIVE 237 123 91 105 75 NC_002967:TDE2361|3end_high-affinity_branched_chain_amino_acid_ABC_transporter,_amino_acid-binding_protein_2395809..2395959_NEGATIVE