Origin IGS: aaattggattctcctgattgtttttaaattgctttgcggaaatcaatataccccgacgcaaagcatcggggtattaaagcctccgcacgaataaaaaaaacttcctcccctttcggaaggaagtttttatcaaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttttgataaaaacttccttccgaaaggggaggaagttttttttattcgtgcggaggctttaataccccgatgctttgcgtcggggtatattgatttccgcaaagcaatttaaaaacaatcaggagaatccaattt Mask Tandem Repeat Region ================================================ aaattggattctcctgattgtttttaaattgctttgcggaaatcaatataccccgacgcaaagcatcggggtattaaagcctccgcacgaataaaaaaaacttcctcccctttcggaaggaagtttttatcaaaaa Find is-nt database================================================ Query_seq: TDE0017:TDE0018|TDE0017:TDE0018:hypothetical protein:LysM domain protein:<-<-:23027..23162 136 aaattggattctcctgattgtttttaaattgctttgcggaaatcaatataccccgacgcaaagcatcggggtattaaagcctccgcacgaataaaaaaaacttcctcccctttcggaaggaagtttttatcaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0017:TDE0018|TDE0017:TDE0018:hypothetical protein:LysM domain protein:<-<-:23027..23162 136 aaattggattctcctgattgtttttaaattgctttgcggaaatcaatataccccgacgcaaagcatcggggtattaaagcctccgcacgaataaaaaaaacttcctcccctttcggaaggaagtttttatcaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0017:TDE0018|TDE0017:TDE0018:hypothetical protein:LysM domain protein:<-<-:23027..23162 136 aaattggattctcctgattgtttttaaattgctttgcggaaatcaatataccccgacgcaaagcatcggggtattaaagcctccgcacgaataaaaaaaacttcctcccctttcggaaggaagtttttatcaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaattggattctcctgattgtttttaaattgctttgcggaaatcaatataccccgacgcaaagcatcggggtattaaagcctccgcacgaataaaaaaaacttcctcccctttcggaaggaagtttttatcaaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 28 End: 135 ........................... M A L R K S I Y P D A K H R G I K A S A R I K K T S S P F G R K F L S K . aaattggattctcctgattgtttttaaattgctttgcggaaatcaatataccccgacgcaaagcatcggggtattaaagcctccgcacgaataaaaaaaacttcctcccctttcggaaggaagtttttatcaaaaa Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaattggattctcctgattgtttttaaattgctttgcggaaatcaatataccccgacgcaaagcatcggggtattaaagcctccgcacgaataaaaaaaacttcctcccctttcggaaggaagtttttatcaaaaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 72 HP_score: -8.4 Tail_Score: -3.53091 Start: 43 End: 78 Full_Region: tattcgtgcggaggc tttaataccccgatgc ttt gcgtcggggtatattga tttccgcaaagcaat ..........................................tttaataccccgatgctttgcgtcggggtatattga.......................................................... TransTerm Strand: - Conf: 95 HP_score: -13.9 Tail_Score: -3.51232 Start: 47 End: 75 Full_Region: tcgtgcggaggcttt aataccccgatgc ttt gcgtcggggtata ttgatttccgcaaag ..............................................aataccccgatgctttgcgtcggggtata............................................................. TransTerm Strand: - Conf: 100 HP_score: -16.5 Tail_Score: -3.33151 Start: 49 End: 73 Full_Region: gtgcggaggctttaa taccccgatgc ttt gcgtcggggta tattgatttccgcaa ................................................taccccgatgctttgcgtcggggta............................................................... Find igs database================================================ Query_seq: TDE0017:TDE0018|TDE0017:TDE0018:hypothetical protein:LysM domain protein:<-<-:23027..23162 136 aaattggattctcctgattgtttttaaattgctttgcggaaatcaatataccccgacgcaaagcatcggggtattaaagcctccgcacgaataaaaaaaacttcctcccctttcggaaggaagtttttatcaaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 136 Len: 136 Subject: NC_002967_TDE0017_TDE0018|hypothetical protein:LysM domain protein|NEGATIVE:NEGATIVE|[23027,23162]|136 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 136 Query Start:1 Query End:136 Subject Strand: POSITIVE Subject Start: 1 Subject End: 136 aaattggattctcctgattgtttttaaattgctttgcggaaatcaatataccccgacgcaaagcatcggggtattaaagcctccgcacgaatnnnnnnnncttcctcccctttcggaaggaagtttttatcaaaaa aaattggattctcctgattgtttttaaattgctttgcggaaatcaatataccccgacgcaaagcatcggggtattaaagcctccgcacgaataaaaaaaacttcctcccctttcggaaggaagtttttatcaaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUGGAUUCUCCUGAUUGUUUUUAAAUUGCUUUGCGGAAAUCAAUAUACCCCGACGCAAAGCAUCGGGGUAUUAAAGCCUCCGCACGAAUAAAAAAAACUUCCUCCCCUUUCGGAAGGAAGUUUUUAUCAAAAA .(((..(......)..)))...............((((((.......(((((((((.((...)).))))))))).......))))))........(((((((((((.((.....)).)))))))))))........ (-42.84) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUGAUAAAAACUUCCUUCCGAAAGGGGAGGAAGUUUUUUUUAUUCGUGCGGAGGCUUUAAUACCCCGAUGCUUUGCGUCGGGGUAUAUUGAUUUCCGCAAAGCAAUUUAAAAACAAUCAGGAGAAUCCAAUUU ((((((((((((((((((((((.....))))))))))))))........(((((((((..((.(((((((((((...)))))))))))))..).))))))))................)))))))).......... (-53.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 999 90 41 181 132 NC_002967:TDE0017|5end_hypothetical_protein_22936..23166_NEGATIVE 745 90 41 172 124 NC_002967:TDE0713|5end_transcription_antitermination_protein,_NusG_family_747109..747339_POSITIVE 697 97 54 207 164 NC_002967:TDE2691|5end_hypothetical_protein_2728838..2729068_POSITIVE 667 97 54 207 164 NC_002967:TDE0830|5end_hypothetical_protein_852025..852255_NEGATIVE 529 74 36 189 151 NC_002967:TDE1194|5end_hypothetical_protein_1224973..1225203_POSITIVE 496 83 41 167 126 NC_002967:TDE0580|5end_hypothetical_protein_615338..615568_POSITIVE 440 73 38 231 197 NC_002967:TDE2498|5end_metallo-beta-lactamase_family_protein_2522961..2523191_NEGATIVE 436 72 46 170 145 NC_002967:TDE0509|5end_hypothetical_protein_560373..560603_NEGATIVE 429 88 41 169 120 NC_002967:TDE1051|5end_hypothetical_protein_1078496..1078726_NEGATIVE 424 80 35 173 122 NC_002967:TDE0371|5end_hypothetical_protein_422687..422917_POSITIVE 418 74 35 152 114 NC_002967:TDE0538|5end_hypothetical_protein_580066..580296_POSITIVE 399 80 35 169 117 NC_002967:TDE0167|5end_ABC_transporter,_ATP-binding_protein_196574..196804_NEGATIVE 388 80 35 171 119 NC_002967:TDE1470|5end_hypothetical_protein_1518026..1518256_NEGATIVE 364 118 77 230 169 NC_002967:TDE1311|5end_ABC_transporter,_ATP-binding/permease_protein_1347371..1347601_POSITIVE 357 72 32 78 41 NC_002967:TDE2690|5end_hypothetical_protein_2728898..2729128_NEGATIVE 323 86 51 65 31 NC_002967:TDE0120|5end_hypothetical_protein_137648..137878_POSITIVE 309 78 31 82 34 NC_002967:TDE2730|5end_hydrolase,_TatD_family_2786586..2786816_POSITIVE 300 73 31 70 34 NC_002967:TDE0317|5end_hypothetical_protein_350656..350886_POSITIVE 294 89 53 66 27 NC_002967:TDE2395|5end_Jag_protein,_putative_2423454..2423684_NEGATIVE 294 125 82 159 97 NC_002967:TDE1910|5end_1-deoxy-D-xylulose-5-phosphate_synthase_1928837..1929067_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 764 90 41 53 6 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 697 97 54 137 94 NC_002967:TDE2689|3end_hypothetical_protein_2728848..2728998_POSITIVE 667 97 54 137 94 NC_002967:TDE0831|3end_hypothetical_protein_852095..852245_NEGATIVE 631 95 54 89 49 NC_002967:TDE2499|3end_hypothetical_protein_2523191..2523341_NEGATIVE 631 95 54 42 2 NC_002967:TDE1052|3end_rubredoxin_1078712..1078862_NEGATIVE 631 95 54 112 72 NC_002967:TDE0710|3end_hypothetical_protein_745667..745817_POSITIVE 631 95 54 65 25 NC_002967:TDE0333|3end_MATE_efflux_family_protein_373083..373233_POSITIVE 606 90 48 50 2 NC_002967:TDE2140|3end_protease_II_2173083..2173233_NEGATIVE 556 96 54 148 107 NC_002967:TDE2459|3end_hypothetical_protein_2485764..2485914_NEGATIVE 551 90 41 66 4 NC_002967:TDE2429|3end_hypothetical_protein_2456628..2456778_NEGATIVE 459 87 48 105 59 NC_002967:TDE0133|3end_transcriptional_regulator,_GntR_family_153202..153352_POSITIVE 451 72 35 74 37 NC_002967:TDE0202|3end_hypothetical_protein_235870..236020_NEGATIVE 436 72 46 130 105 NC_002967:TDE0510|3end_hypothetical_protein_560413..560563_NEGATIVE 424 80 35 76 25 NC_002967:TDE0711|3end_hypothetical_protein_745690..745840_NEGATIVE 418 74 35 84 46 NC_002967:TDE0537|3end_hypothetical_protein_580078..580228_POSITIVE 399 80 35 76 24 NC_002967:TDE0168|3end_transcriptional_regulator,_GntR_family_196667..196817_NEGATIVE 385 87 48 60 13 NC_002967:TDE1471|3end_hypothetical_protein_1518145..1518295_NEGATIVE 364 118 77 119 58 NC_002967:TDE1310|3end_modulator_of_DNA_gyrase_family_protein_1347340..1347490_POSITIVE 332 59 13 122 79 NC_002967:TDE2458|3end_hypothetical_protein_2485849..2485999_POSITIVE 324 72 35 42 1 NC_002967:TDE2139|3end_hypothetical_protein_2172897..2173047_POSITIVE