Origin IGS: atttttctgttattgatattgtatttcagtttttgactgtctgcaaaagtaagtatttcgttcctgtcgaggggtaggagagcagggaagcacctgtcttattccc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gggaataagacaggtgcttccctgctctcctacccctcgacaggaacgaaatacttacttttgcagacagtcaaaaactgaaatacaatatcaataacagaaaaat Mask Tandem Repeat Region ================================================ atttttctgttattgatattgtatttcagtttttgactgtctgcaaaagtaagtatttcgttcctgtcgaggggtaggagagcagggaagcacctgtcttattccc Find is-nt database================================================ Query_seq: PG0482:PG0483|PG0482:PG0483:hypothetical protein:kinase, putative:<-<-:523220..523325 106 atttttctgttattgatattgtatttcagtttttgactgtctgcaaaagtaagtatttcgttcctgtcgaggggtaggagagcagggaagcacctgtcttattccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0482:PG0483|PG0482:PG0483:hypothetical protein:kinase, putative:<-<-:523220..523325 106 atttttctgttattgatattgtatttcagtttttgactgtctgcaaaagtaagtatttcgttcctgtcgaggggtaggagagcagggaagcacctgtcttattccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0482:PG0483|PG0482:PG0483:hypothetical protein:kinase, putative:<-<-:523220..523325 106 atttttctgttattgatattgtatttcagtttttgactgtctgcaaaagtaagtatttcgttcctgtcgaggggtaggagagcagggaagcacctgtcttattccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttttctgttattgatattgtatttcagtttttgactgtctgcaaaagtaagtatttcgttcctgtcgaggggtaggagagcagggaagcacctgtcttattccc Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 13 End: 102 ............ Q Y Q I E T K S Q R C F Y T N R E Q R P T P S C P L V Q R M .... atttttctgttattgatattgtatttcagtttttgactgtctgcaaaagtaagtatttcgttcctgtcgaggggtaggagagcagggaagcacctgtcttattccc 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================================================ atttttctgttattgatattgtatttcagtttttgactgtctgcaaaagtaagtatttcgttcctgtcgaggggtaggagagcagggaagcacctgtcttattccc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0482:PG0483|PG0482:PG0483:hypothetical protein:kinase, putative:<-<-:523220..523325 106 atttttctgttattgatattgtatttcagtttttgactgtctgcaaaagtaagtatttcgttcctgtcgaggggtaggagagcagggaagcacctgtcttattccc Intra-Species Hit: Count: 1 Min: 1 Max: 106 Len: 106 Subject: NC_002950_PG0482_PG0483|hypothetical protein:kinase, putative|NEGATIVE:NEGATIVE|[523220,523325]|106 HSP 1 e-value: 6.0E-54 bit: 210.0 Len: 106 Query Start:1 Query End:106 Subject Strand: POSITIVE Subject Start: 1 Subject End: 106 atttttctgttattgatattgtatttcagtttttgactgtctgcaaaagtaagtatttcgttcctgtcgaggggtaggagagcagggaagcacctgtcttattccc atttttctgttattgatattgtatttcagtttttgactgtctgcaaaagtaagtatttcgttcctgtcgaggggtaggagagcagggaagcacctgtcttattccc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUUCUGUUAUUGAUAUUGUAUUUCAGUUUUUGACUGUCUGCAAAAGUAAGUAUUUCGUUCCUGUCGAGGGGUAGGAGAGCAGGGAAGCACCUGUCUUAUUCCC .........(((((....(((((...(((((...)))))..))))).))))).....(((.......))).(((...((((.((((......))))))))...))) (-22.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGAAUAAGACAGGUGCUUCCCUGCUCUCCUACCCCUCGACAGGAACGAAAUACUUACUUUUGCAGACAGUCAAAAACUGAAAUACAAUAUCAAUAACAGAAAAAU (((....(((((((......)))).)))....))).(((.......)))..................((((.....)))).......................... (-13.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1019 100 51 191 142 NC_002950:PG0482|5end_hypothetical_protein_523129..523359_NEGATIVE 413 97 57 147 103 NC_002950:PG0985|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1046930..1047160_POSITIVE 385 98 53 77 19 NC_002950:PG1977|5end_hypothetical_protein_2066693..2066923_NEGATIVE 362 97 52 67 26 NC_002950:PG1337|5end_umuD_protein_1417813..1418043_POSITIVE 355 91 58 55 22 NC_002950:PG0275|5end_thioredoxin_family_protein_307464..307694_NEGATIVE 347 97 61 73 32 NC_002950:PG2114|5end_hypothetical_protein_2224158..2224388_NEGATIVE 343 76 31 189 145 NC_002950:PG0224|5end_hypothetical_protein_258252..258482_NEGATIVE 339 99 55 63 4 NC_002950:PG1006|5end_hypothetical_protein_1066478..1066708_NEGATIVE 338 98 60 227 186 NC_002950:PG1555|5end_hypothetical_protein_1636011..1636241_POSITIVE 338 99 52 63 6 NC_002950:PG0558|5end_purine_nucleoside_phosphorylase_616331..616561_NEGATIVE 332 90 41 100 49 NC_002950:PG0210|5end_precorrin-6x_reductase/cobalamin_biosynthetic_protein_CbiD_245969..246199_NEGATIVE 331 89 41 83 34 NC_002950:PG0855|5end_hypothetical_protein_916055..916285_NEGATIVE 331 98 54 77 26 NC_002950:PG0306|5end_electron_transport_complex,_RnfABCDGE_type,_G_subunit_341916..342146_POSITIVE 328 99 55 192 154 NC_002950:PG2201|5end_peptide_deformylase_2309412..2309642_NEGATIVE 325 99 58 216 153 NC_002950:PG0109|5end_hypothetical_protein_131331..131561_POSITIVE 322 98 55 53 10 NC_002950:PG1592|5end_HDIG_domain_protein_1669383..1669613_POSITIVE 318 90 41 144 88 NC_002950:PG0490|5end_hypothetical_protein_530828..531058_POSITIVE 315 86 41 74 26 NC_002950:PG1543|5end_thioesterase_family_protein_1622088..1622318_POSITIVE 315 98 65 44 11 NC_002950:PG0147|5end_hypothetical_protein_169667..169897_NEGATIVE 314 90 41 98 48 NC_002950:PG0736|5end_ribonuclease_HII_785608..785838_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 384 98 63 47 2 NC_002950:PG1978|3end_hypothetical_protein_2066723..2066873_NEGATIVE 370 92 56 151 115 NC_002950:PG1706|3end_hypothetical_protein_1793849..1793999_NEGATIVE 353 97 51 69 14 NC_002950:PG1964|3end_bacterial_sugar_transferase_2054396..2054546_POSITIVE 353 91 61 87 58 NC_002950:PG0678|3end_pyrazinamidase/nicotinamidase,_putative_729471..729621_POSITIVE 349 98 58 79 14 NC_002950:PG0739|3end_ribonuclease_Z_787941..788091_POSITIVE 333 89 43 59 13 NC_002950:PG0452|3end_hypothetical_protein_495106..495256_POSITIVE 332 90 41 103 52 NC_002950:PG0211|3end_cobalamin_biosynthesis_protein_CbiG/precorrin-4_C11-methyltransferase_245966..246116_NEGATIVE 328 99 55 87 49 NC_002950:PG2202|3end_Holliday_junction_resolvase-like_protein_2309517..2309667_NEGATIVE 322 96 53 105 53 NC_002950:PG1232|3end_glutamate_dehydrogenase_1308274..1308424_NEGATIVE 319 96 58 146 104 NC_002950:PG0030|3end_cytidine_deaminase_36402..36552_POSITIVE 318 95 51 97 52 NC_002950:PG1087|3end_radical_SAM_protein,_TIGR01212_family_1154820..1154970_POSITIVE 315 98 65 57 24 NC_002950:PG0148|3end_sigma-54-dependent_transcriptional_regulator_169654..169804_NEGATIVE 314 90 41 87 37 NC_002950:PG0735|3end_aminotransferase,_class_V_785677..785827_POSITIVE 313 99 53 60 3 NC_002950:PG0496|3end_hypothetical_protein_537340..537490_POSITIVE 308 97 65 118 76 NC_002950:PG1587|3end_PAP2_superfamily_protein_1665779..1665929_POSITIVE 308 100 59 106 50 NC_002950:PG1494|3end_hypothetical_protein_1571234..1571384_POSITIVE 308 92 56 66 27 NC_002950:PG1463|3end_hypothetical_protein_1541471..1541621_POSITIVE 307 92 58 72 37 NC_002950:PG1581|3end_hypothetical_protein_1659404..1659554_POSITIVE 307 98 56 50 1 NC_002950:PG0305|3end_electron_transport_complex,_RnfABCDGE_type,_D_subunit_341969..342119_POSITIVE 306 99 58 130 91 NC_002950:PG0399|3end_lipoprotein,_putative_435707..435857_NEGATIVE