Origin IGS: tgagcaaaaacaccggaagccgcagggtaatgaactgtgatgcagtgagctgccctgcggcttcttttataaaagactgttcaatcagcctccggcagtggaggcataaatagaggaaaac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gttttcctctatttatgcctccactgccggaggctgattgaacagtcttttataaaagaagccgcagggcagctcactgcatcacagttcattaccctgcggcttccggtgtttttgctca Mask Tandem Repeat Region ================================================ tgagcaaaaacaccggaagccgcagggtaatgaactgtgatgcagtgagctgccctgcggcttcttttataaaagactgttcaatcagcctccggcagtggaggcataaatagaggaaaac Find is-nt database================================================ Query_seq: TF1296:TF1297|TF1296:TF1297:possible DNA-binding protein, histone-like family:hypothetical protein:->->:1379043..1379163 121 tgagcaaaaacaccggaagccgcagggtaatgaactgtgatgcagtgagctgccctgcggcttcttttataaaagactgttcaatcagcctccggcagtggaggcataaatagaggaaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1296:TF1297|TF1296:TF1297:possible DNA-binding protein, histone-like family:hypothetical protein:->->:1379043..1379163 121 tgagcaaaaacaccggaagccgcagggtaatgaactgtgatgcagtgagctgccctgcggcttcttttataaaagactgttcaatcagcctccggcagtggaggcataaatagaggaaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1296:TF1297|TF1296:TF1297:possible DNA-binding protein, histone-like family:hypothetical protein:->->:1379043..1379163 121 tgagcaaaaacaccggaagccgcagggtaatgaactgtgatgcagtgagctgccctgcggcttcttttataaaagactgttcaatcagcctccggcagtggaggcataaatagaggaaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgagcaaaaacaccggaagccgcagggtaatgaactgtgatgcagtgagctgccctgcggcttcttttataaaagactgttcaatcagcctccggcagtggaggcataaatagaggaaaac Predict ORF larger than 30AA ================================================ tgagcaaaaacaccggaagccgcagggtaatgaactgtgatgcagtgagctgccctgcggcttcttttataaaagactgttcaatcagcctccggcagtggaggcataaatagaggaaaac 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================================================ tgagcaaaaacaccggaagccgcagggtaatgaactgtgatgcagtgagctgccctgcggcttcttttataaaagactgttcaatcagcctccggcagtggaggcataaatagaggaaaac Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -15.3 Tail_Score: -4.3739 Start: 16 End: 64 Full_Region: TGAGCAAAAACACCG GAAGCCGCAGGGTAATGAACTGT GAT GCAGTGAGCTGCCCTGCGGCTTC TTTTATAAAAGACTG ...............GAAGCCGCAGGGTAATGAACTGTGATGCAGTGAGCTGCCCTGCGGCTTC......................................................... Find igs database================================================ Query_seq: TF1296:TF1297|TF1296:TF1297:possible DNA-binding protein, histone-like family:hypothetical protein:->->:1379043..1379163 121 tgagcaaaaacaccggaagccgcagggtaatgaactgtgatgcagtgagctgccctgcggcttcttttataaaagactgttcaatcagcctccggcagtggaggcataaatagaggaaaac Intra-Species Hit: Count: 1 Min: 1 Max: 121 Len: 121 Subject: tfor_TF1296_TF1297|possible DNA-binding protein, histone-like family:hypothetical protein|POSITIVE:POSITIVE|[1379043,1379163]|121 HSP 1 e-value: 8.0E-63 bit: 240.0 Len: 121 Query Start:1 Query End:121 Subject Strand: POSITIVE Subject Start: 1 Subject End: 121 tgagcaaaaacaccggaagccgcagggtaatgaactgtgatgcagtgagctgccctgcggcttcttttataaaagactgttcaatcagcctccggcagtggaggcataaatagaggaaaac tgagcaaaaacaccggaagccgcagggtaatgaactgtgatgcagtgagctgccctgcggcttcttttataaaagactgttcaatcagcctccggcagtggaggcataaatagaggaaaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGCAAAAACACCGGAAGCCGCAGGGUAAUGAACUGUGAUGCAGUGAGCUGCCCUGCGGCUUCUUUUAUAAAAGACUGUUCAAUCAGCCUCCGGCAGUGGAGGCAUAAAUAGAGGAAAAC ((((((........(((((((((((((((.(..((((.....))))..).)))))))))))))))............))))))....(((((((....)))))))................ (-50.75) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUUCCUCUAUUUAUGCCUCCACUGCCGGAGGCUGAUUGAACAGUCUUUUAUAAAAGAAGCCGCAGGGCAGCUCACUGCAUCACAGUUCAUUACCCUGCGGCUUCCGGUGUUUUUGCUCA .......((.(((...((((((......)))))).))).))..(((.....(((...((((((((((((......((((.....))))......))))))))))))...)))....))).. (-41.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 427 60 14 181 120 tfor:TF0027|5end_conserved_hypothetical_protein_22866..23096_POSITIVE 419 59 13 210 150 tfor:TF2466|5end_pyruvate_kinase_2644385..2644615_POSITIVE 412 59 14 60 12 tfor:TF0996|5end_ribonuclease_D_1050882..1051112_POSITIVE 388 60 11 153 106 tfor:TF0310|5end_conserved_hypothetical_protein_334685..334915_POSITIVE 378 60 13 59 5 tfor:TF3024|5end_periplasmic_protease_3247204..3247434_POSITIVE 376 60 14 229 173 tfor:TF0376|5end_conserved_hypothetical_protein_394303..394533_POSITIVE 375 56 14 54 3 tfor:TF1409|5end_outer_membrane_protein_TolC_1485479..1485709_POSITIVE 372 60 15 184 144 tfor:TF0529|5end_transposase_554776..555006_POSITIVE 369 60 13 152 107 tfor:TF2499|5end_possible_thioesterase_family_protein_2673903..2674133_POSITIVE 368 60 15 206 169 tfor:TF1570|5end_ATP_synthase_subunit_A_1678325..1678555_POSITIVE 363 100 52 215 168 tfor:TF0758|5end_peptidyl-tRNA_hydrolase_805307..805537_POSITIVE 362 58 11 210 172 tfor:TF3000|5end_hypothetical_protein_3216412..3216642_POSITIVE 362 58 11 210 172 tfor:TF2825|5end_transposase_3016390..3016620_POSITIVE 362 58 11 210 172 tfor:TF2591|5end_transposase_2757641..2757871_POSITIVE 362 58 11 210 172 tfor:TF2110|5end_transposase_2279217..2279447_POSITIVE 362 58 11 210 172 tfor:TF0942|5end_transposase_982998..983228_POSITIVE 362 58 11 210 172 tfor:TF0716|5end_transposase_766297..766527_POSITIVE 359 60 12 151 95 tfor:TF0204|5end_cation_efflux_system_protein_230618..230848_POSITIVE 352 60 16 219 167 tfor:TF1554|5end_UDP-glucose_dehydrogenase_1659623..1659853_POSITIVE 351 68 26 171 135 tfor:TF2115|5end_conserved_hypothetical_protein;_possible_carboxylesterase_2284786..2285016_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 468 64 21 75 32 tfor:TF1296|3end_possible_DNA-binding_protein,_histone-like_family_1378982..1379132_POSITIVE 412 59 14 60 12 tfor:TF0995|3end_conserved_hypothetical_protein_1050962..1051112_POSITIVE 378 60 13 76 22 tfor:TF3022|3end_chorismate_synthase_3247301..3247451_POSITIVE 372 60 15 107 67 tfor:TF0528|3end_two-component_system_sensor_histidine_kinase_554779..554929_POSITIVE 369 60 13 54 9 tfor:TF2498|3end_electron_transfer_flavoprotein,_alpha_subunit_2673885..2674035_POSITIVE 363 100 52 121 74 tfor:TF0757|3end_50S_ribosomal_protein_L25;_general_stress_protein_805293..805443_POSITIVE 362 58 11 55 17 tfor:TF2590|3end_transposase_2757566..2757716_POSITIVE 359 60 12 113 57 tfor:TF0203|3end_PhoH-like_protein_230660..230810_POSITIVE 347 58 12 60 11 tfor:TF0593|3end_membrane-associated_phospholipid_phosphatase_627051..627201_POSITIVE 340 61 26 145 105 tfor:TF1681|3end_dTDP-4-keto-L-rhamnose_reductase_1795844..1795994_POSITIVE 339 50 2 73 29 tfor:TF2058|3end_possible_ATP-dependent_DNA_helicase_2223798..2223948_POSITIVE 336 61 23 102 61 tfor:TF2718|3end_hypothetical_protein_2892811..2892961_POSITIVE 336 61 21 105 62 tfor:TF2173|3end_hypothetical_protein_2346063..2346213_POSITIVE 336 61 21 105 62 tfor:TF0346|3end_hypothetical_protein_367316..367466_POSITIVE 336 44 10 149 115 tfor:TF0309|3end_conserved_hypothetical_protein_334775..334925_POSITIVE 333 58 14 97 40 tfor:TF0008|3end_hypothetical_protein_4336..4486_POSITIVE 331 60 14 151 97 tfor:TF0390|3end_conserved_hypothetical_protein_410068..410218_POSITIVE 327 60 14 51 4 tfor:TF0825|3end_hypothetical_protein_883850..884000_POSITIVE 325 61 23 74 23 tfor:TF2171|3end_hypothetical_protein_2345792..2345942_POSITIVE 323 55 14 151 96 tfor:TF0026|3end_hypothetical_protein_22922..23072_POSITIVE