Origin IGS: ttcctgccaaactcctaaattttcgccggatatttcattgattgaggccgccgagatttcgtttcgataaaaatccatggcttcggttcgtatttctttaattgacttgtcattttcttgggcaaaaacttgagtatagccctgaaaaagcgttaaaatgagagtaaaacaacaaagtttccgtataaattttcttttcatcatttgcatataatagcacaatatcggatttttagcaagattttcgcattgggttttgtatcaatggcaatacatatcga .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcgatatgtattgccattgatacaaaacccaatgcgaaaatcttgctaaaaatccgatattgtgctattatatgcaaatgatgaaaagaaaatttatacggaaactttgttgttttactctcattttaacgctttttcagggctatactcaagtttttgcccaagaaaatgacaagtcaattaaagaaatacgaaccgaagccatggatttttatcgaaacgaaatctcggcggcctcaatcaatgaaatatccggcgaaaatttaggagtttggcaggaa Mask Tandem Repeat Region ================================================ ttcctgccaaactcctaaattttcgccggatatttcattgattgaggccgccgagatttcgtttcgataaaaatccatggcttcggttcgtatttctttaattgacttgtcattttcttgggcaaaaacttgagtatagccctgaaaaagcgttaaaatgagagtaaaacaacaaagtttccgtataaattttcttttcatcatttgcatataatagcacaatatcggatttttagcaagattttcgcattgggttttgtatcaatggcaatacatatcga Find is-nt database================================================ Query_seq: TDE1372:TDE1373|TDE1372:TDE1373:hypothetical protein:HD domain protein:<-<-:1416988..1417268 281 ttcctgccaaactcctaaattttcgccggatatttcattgattgaggccgccgagatttcgtttcgataaaaatccatggcttcggttcgtatttctttaattgacttgtcattttcttgggcaaaaacttgagtatagccctgaaaaagcgttaaaatgagagtaaaacaacaaagtttccgtataaattttcttttcatcatttgcatataatagcacaatatcggatttttagcaagattttcgcattgggttttgtatcaatggcaatacatatcga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1372:TDE1373|TDE1372:TDE1373:hypothetical protein:HD domain protein:<-<-:1416988..1417268 281 ttcctgccaaactcctaaattttcgccggatatttcattgattgaggccgccgagatttcgtttcgataaaaatccatggcttcggttcgtatttctttaattgacttgtcattttcttgggcaaaaacttgagtatagccctgaaaaagcgttaaaatgagagtaaaacaacaaagtttccgtataaattttcttttcatcatttgcatataatagcacaatatcggatttttagcaagattttcgcattgggttttgtatcaatggcaatacatatcga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1372:TDE1373|TDE1372:TDE1373:hypothetical protein:HD domain protein:<-<-:1416988..1417268 281 ttcctgccaaactcctaaattttcgccggatatttcattgattgaggccgccgagatttcgtttcgataaaaatccatggcttcggttcgtatttctttaattgacttgtcattttcttgggcaaaaacttgagtatagccctgaaaaagcgttaaaatgagagtaaaacaacaaagtttccgtataaattttcttttcatcatttgcatataatagcacaatatcggatttttagcaagattttcgcattgggttttgtatcaatggcaatacatatcga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcctgccaaactcctaaattttcgccggatatttcattgattgaggccgccgagatttcgtttcgataaaaatccatggcttcggttcgtatttctttaattgacttgtcattttcttgggcaaaaacttgagtatagccctgaaaaagcgttaaaatgagagtaaaacaacaaagtttccgtataaattttcttttcatcatttgcatataatagcacaatatcggatttttagcaagattttcgcattgggttttgtatcaatggcaatacatatcga Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: - Start: 113 End: 223 ................................................................................................................ K R P C F S S Y L G S F A N F H S Y F L L T E T Y I K K E D N A Y L L V M .......................................................... Protein_Len: 40 Strand: - Start: 18 End: 137 ................. I K A P Y K M S Q P R R S K T E I F I W P K P E Y K K L Q S T M K K P L F K L M ................................................................................................................................................ Protein_Len: 60 Strand: - Start: 1 End: 225 A A S I E N R Y F D M A E T R I E K I S K D N E Q A F V Q T Y G Q F L T L I L T F C C L K R I F K R K M M Q M Y Y C L M ........................................................ ttcctgccaaactcctaaattttcgccggatatttcattgattgaggccgccgagatttcgtttcgataaaaatccatggcttcggttcgtatttctttaattgacttgtcattttcttgggcaaaaacttgagtatagccctgaaaaagcgttaaaatgagagtaaaacaacaaagtttccgtataaattttcttttcatcatttgcatataatagcacaatatcggatttttagcaagattttcgcattgggttttgtatcaatggcaatacatatcga 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: 86 Start: 211 End: 240 ..................................................................................................................................................................................................................CTTGCTAAAAATCCGATATTGTGCTATTAT......................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttcctgccaaactcctaaattttcgccggatatttcattgattgaggccgccgagatttcgtttcgataaaaatccatggcttcggttcgtatttctttaattgacttgtcattttcttgggcaaaaacttgagtatagccctgaaaaagcgttaaaatgagagtaaaacaacaaagtttccgtataaattttcttttcatcatttgcatataatagcacaatatcggatttttagcaagattttcgcattgggttttgtatcaatggcaatacatatcga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1372:TDE1373|TDE1372:TDE1373:hypothetical protein:HD domain protein:<-<-:1416988..1417268 281 ttcctgccaaactcctaaattttcgccggatatttcattgattgaggccgccgagatttcgtttcgataaaaatccatggcttcggttcgtatttctttaattgacttgtcattttcttgggcaaaaacttgagtatagccctgaaaaagcgttaaaatgagagtaaaacaacaaagtttccgtataaattttcttttcatcatttgcatataatagcacaatatcggatttttagcaagattttcgcattgggttttgtatcaatggcaatacatatcga Intra-Species Hit: Count: 1 Min: 1 Max: 281 Len: 281 Subject: NC_002967_TDE1372_TDE1373|hypothetical protein:HD domain protein|NEGATIVE:NEGATIVE|[1416988,1417268]|281 HSP 1 e-value: 1.0E-158 bit: 557.0 Len: 281 Query Start:1 Query End:281 Subject Strand: POSITIVE Subject Start: 1 Subject End: 281 ttcctgccaaactcctaaattttcgccggatatttcattgattgaggccgccgagatttcgtttcgataaaaatccatggcttcggttcgtatttctttaattgacttgtcattttcttgggcaaaaacttgagtatagccctgaaaaagcgttaaaatgagagtaaaacaacaaagtttccgtataaattttcttttcatcatttgcatataatagcacaatatcggatttttagcaagattttcgcattgggttttgtatcaatggcaatacatatcga ttcctgccaaactcctaaattttcgccggatatttcattgattgaggccgccgagatttcgtttcgataaaaatccatggcttcggttcgtatttctttaattgacttgtcattttcttgggcaaaaacttgagtatagccctgaaaaagcgttaaaatgagagtaaaacaacaaagtttccgtataaattttcttttcatcatttgcatataatagcacaatatcggatttttagcaagattttcgcattgggttttgtatcaatggcaatacatatcga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCCUGCCAAACUCCUAAAUUUUCGCCGGAUAUUUCAUUGAUUGAGGCCGCCGAGAUUUCGUUUCGAUAAAAAUCCAUGGCUUCGGUUCGUAUUUCUUUAAUUGACUUGUCAUUUUCUUGGGCAAAAACUUGAGUAUAGCCCUGAAAAAGCGUUAAAAUGAGAGUAAAACAACAAAGUUUCCGUAUAAAUUUUCUUUUCAUCAUUUGCAUAUAAUAGCACAAUAUCGGAUUUUUAGCAAGAUUUUCGCAUUGGGUUUUGUAUCAAUGGCAAUACAUAUCGA ....(((((...(((.((((((....((((.((((.((.(((((((((((..((....(((...)))......))..))))))))))).))..(((((...(((((..((..(((((..((((....((....))...)))).))))).)))))))...)))))..........)))).))))...)))))).............(((........))).......)))......(((((((((.......))))))))).....)))))........... (-51.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGAUAUGUAUUGCCAUUGAUACAAAACCCAAUGCGAAAAUCUUGCUAAAAAUCCGAUAUUGUGCUAUUAUAUGCAAAUGAUGAAAAGAAAAUUUAUACGGAAACUUUGUUGUUUUACUCUCAUUUUAACGCUUUUUCAGGGCUAUACUCAAGUUUUUGCCCAAGAAAAUGACAAGUCAAUUAAAGAAAUACGAACCGAAGCCAUGGAUUUUUAUCGAAACGAAAUCUCGGCGGCCUCAAUCAAUGAAAUAUCCGGCGAAAAUUUAGGAGUUUGGCAGGAA ..........((((.((((..........))))))))...((((((((((..(((..((((.(((........)))...))))......((((((...((((.(.((..(((.................((...((((.((((...((....))....)))).......(((....)))......))))..))....((.(((.((((((((.........)))))).))..))).))...)))..)).).))))....)))))).))).)))))))))). (-54.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 961 90 41 181 132 NC_002967:TDE1372|5end_hypothetical_protein_1416897..1417127_NEGATIVE 380 269 225 127 81 NC_002967:TDE1084|5end_folylpolyglutamate_synthetase,_putative_1116286..1116516_NEGATIVE 328 49 1 203 144 NC_002967:TDE0741|5end_hypothetical_protein_778158..778388_NEGATIVE 322 66 27 230 194 NC_002967:TDE2007|5end_ABC_transporter,_ATP-binding/permease_protein_2026819..2027049_POSITIVE 317 89 47 102 43 NC_002967:TDE1139|5end_hypothetical_protein_1168615..1168845_NEGATIVE 313 90 46 70 21 NC_002967:TDE0538|5end_hypothetical_protein_580066..580296_POSITIVE 303 53 14 56 6 NC_002967:TDE2485|5end_hypothetical_protein_2509123..2509353_NEGATIVE 292 87 42 101 54 NC_002967:TDE2586|5end_DNA_polymerase_III_subunits_gamma_and_tau_2622089..2622319_NEGATIVE 290 89 41 112 47 NC_002967:TDE1638|5end_dephospho-CoA_kinase,_putative_1688882..1689112_POSITIVE 288 50 3 116 77 NC_002967:TDE2149|5end_transglycosylase,_SLT_family_2187293..2187523_NEGATIVE 284 64 23 101 50 NC_002967:TDE2637|5end_hypothetical_protein_2677316..2677546_NEGATIVE 282 68 22 225 181 NC_002967:TDE0273|5end_ABC_transporter,_ATP-binding/permease_protein_304633..304863_NEGATIVE 281 82 45 158 124 NC_002967:TDE1885|5end_hypothetical_protein_1906857..1907087_POSITIVE 280 53 11 68 21 NC_002967:TDE2736|5end_hypothetical_protein_2791812..2792042_NEGATIVE 280 60 13 46 9 NC_002967:TDE1105|5end_ribosome-binding_factor_A_1138199..1138429_NEGATIVE 279 55 13 182 142 NC_002967:TDE0644|5end_ABC_transporter,_ATP-binding_protein_680576..680806_NEGATIVE 277 125 82 119 77 NC_002967:TDE1542|5end_hypothetical_protein_1585857..1586087_POSITIVE 275 89 45 45 3 NC_002967:TDE1236|5end_triosephosphate_isomerase_1269486..1269716_POSITIVE 275 69 27 190 134 NC_002967:TDE1021|5end_lipoprotein,_putative_1053564..1053794_NEGATIVE 274 63 21 231 187 NC_002967:TDE2126|5end_hypothetical_protein_2159533..2159763_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 338 69 27 121 69 NC_002967:TDE1056|3end_hypothetical_protein_1085895..1086045_POSITIVE 320 89 42 109 51 NC_002967:TDE2571|3end_hypothetical_protein_2597922..2598072_NEGATIVE 315 88 45 53 8 NC_002967:TDE0741|3end_hypothetical_protein_776185..776335_NEGATIVE 309 78 38 134 86 NC_002967:TDE2610|3end_hypothetical_protein_2651854..2652004_NEGATIVE 290 89 41 112 47 NC_002967:TDE1637|3end_DNA_polymerase_I_1688962..1689112_POSITIVE 283 64 21 150 105 NC_002967:TDE2125|3end_leucyl/phenylalanyl-tRNA--protein_transferase_2159531..2159681_POSITIVE 280 60 13 53 16 NC_002967:TDE1106|3end_translation_initiation_factor_IF-2_1138192..1138342_NEGATIVE 277 48 1 144 97 NC_002967:TDE2265|3end_hypothetical_protein_2302634..2302784_POSITIVE 277 125 82 122 80 NC_002967:TDE1541|3end_metallo-beta-lactamase_family_protein_1585940..1586090_POSITIVE 274 85 45 33 1 NC_002967:TDE0143|3end_thiamine_ABC_transporter,_thiamine-binding_protein_165103..165253_POSITIVE 268 60 12 144 102 NC_002967:TDE1293|3end_TldD/PmbA_family_protein_1330621..1330771_NEGATIVE 267 90 47 63 21 NC_002967:TDE1847|3end_hypothetical_protein_1875845..1875995_POSITIVE 266 90 49 55 4 NC_002967:TDE0739|3end_hypothetical_protein_776028..776178_POSITIVE 264 169 121 58 8 NC_002967:TDE2183|3end_hypothetical_protein_2215935..2216085_POSITIVE 263 51 18 56 26 NC_002967:TDE2707|3end_hypothetical_protein_2754929..2755079_POSITIVE 261 90 46 77 24 NC_002967:TDE0845|3end_conserved_hypothetical_protein_TIGR00266_868549..868699_POSITIVE 259 66 21 77 37 NC_002967:TDE0635|3end_hypothetical_protein_670578..670728_POSITIVE 258 87 47 60 16 NC_002967:TDE1049|3end_elongation_factor_EF-2_1077454..1077604_POSITIVE 258 59 12 81 36 NC_002967:TDE0766|3end_30S_ribosomal_protein_S10_806372..806522_POSITIVE 257 100 52 41 2 NC_002967:TDE2604|3end_hypothetical_protein_2644224..2644374_NEGATIVE