Origin IGS: tagagaaaagatggatgatagggaacaaaaattccaatcagccatcgcgttaagggcttcctgccataaccaaaagagaccgagacattttgtcccggcctctttttatatttaaccttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaggttaaatataaaaagaggccgggacaaaatgtctcggtctcttttggttatggcaggaagcccttaacgcgatggctgattggaatttttgttccctatcatccatcttttctcta Mask Tandem Repeat Region ================================================ tagagaaaagatggatgatagggaacaaaaattccaatcagccatcgcgttaagggcttcctgccataaccaaaagagaccgagacattttgtcccggcctctttttatatttaaccttt Find is-nt database================================================ Query_seq: SSA_1907:SSA_1909|SSA_1907:SSA_1909:hypothetical protein:Transcriptional attenuator LytR, putative:-><-:1900874..1900993 120 tagagaaaagatggatgatagggaacaaaaattccaatcagccatcgcgttaagggcttcctgccataaccaaaagagaccgagacattttgtcccggcctctttttatatttaaccttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1907:SSA_1909|SSA_1907:SSA_1909:hypothetical protein:Transcriptional attenuator LytR, putative:-><-:1900874..1900993 120 tagagaaaagatggatgatagggaacaaaaattccaatcagccatcgcgttaagggcttcctgccataaccaaaagagaccgagacattttgtcccggcctctttttatatttaaccttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1907:SSA_1909|SSA_1907:SSA_1909:hypothetical protein:Transcriptional attenuator LytR, putative:-><-:1900874..1900993 120 tagagaaaagatggatgatagggaacaaaaattccaatcagccatcgcgttaagggcttcctgccataaccaaaagagaccgagacattttgtcccggcctctttttatatttaaccttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagagaaaagatggatgatagggaacaaaaattccaatcagccatcgcgttaagggcttcctgccataaccaaaagagaccgagacattttgtcccggcctctttttatatttaaccttt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 11 End: 112 .......... M D D R E Q K F Q S A I A L R A S C H N Q K R P R H F V P A S F Y I ........ tagagaaaagatggatgatagggaacaaaaattccaatcagccatcgcgttaagggcttcctgccataaccaaaagagaccgagacattttgtcccggcctctttttatatttaaccttt 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================================================ tagagaaaagatggatgatagggaacaaaaattccaatcagccatcgcgttaagggcttcctgccataaccaaaagagaccgagacattttgtcccggcctctttttatatttaaccttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -10.8 Tail_Score: -5.19879 Start: 76 End: 102 Full_Region: CTGCCATAACCAAAA GAGACCGAGACA TTT TGTCCCGGCCTC TTTTTATATTTAACC ...........................................................................GAGACCGAGACATTTTGTCCCGGCCTC.................. Find igs database================================================ Query_seq: SSA_1907:SSA_1909|SSA_1907:SSA_1909:hypothetical protein:Transcriptional attenuator LytR, putative:-><-:1900874..1900993 120 tagagaaaagatggatgatagggaacaaaaattccaatcagccatcgcgttaagggcttcctgccataaccaaaagagaccgagacattttgtcccggcctctttttatatttaaccttt Intra-Species Hit: Count: 1 Min: 1 Max: 120 Len: 120 Subject: NC_009009_SSA_1907_SSA_1909|hypothetical protein:Transcriptional attenuator LytR, putative|POSITIVE:NEGATIVE|[1900874,1900993]|120 HSP 1 e-value: 3.0E-62 bit: 238.0 Len: 120 Query Start:1 Query End:120 Subject Strand: POSITIVE Subject Start: 1 Subject End: 120 tagagaaaagatggatgatagggaacaaaaattccaatcagccatcgcgttaagggcttcctgccataaccaaaagagaccgagacattttgtcccggcctctttttatatttaaccttt tagagaaaagatggatgatagggaacaaaaattccaatcagccatcgcgttaagggcttcctgccataaccaaaagagaccgagacattttgtcccggcctctttttatatttaaccttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAGAAAAGAUGGAUGAUAGGGAACAAAAAUUCCAAUCAGCCAUCGCGUUAAGGGCUUCCUGCCAUAACCAAAAGAGACCGAGACAUUUUGUCCCGGCCUCUUUUUAUAUUUAACCUUU .........(((((.((((.((((.......)))).)))).)))))..(((((.(((.....)))......(((((((.(((.(((.....))).))).))))))).....))))).... (-36.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGGUUAAAUAUAAAAAGAGGCCGGGACAAAAUGUCUCGGUCUCUUUUGGUUAUGGCAGGAAGCCCUUAACGCGAUGGCUGAUUGGAAUUUUUGUUCCCUAUCAUCCAUCUUUUCUCUA ..............(((((((((((((((.....))))))))))))))).((((.(((.....)))..))))..(((((.((((.(((((....)))))..)))).)))))......... (-46.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 399 102 61 137 95 NC_009009:SSA_0680|5end_Serine/threonine_protein_phosphatase,_putative_662425..662655_POSITIVE 359 100 51 64 21 NC_009009:SSA_0468|5end_Precorrin-6y_C5,15-methyltransferase-like,_putative_471706..471936_POSITIVE 333 109 62 221 174 NC_009009:SSA_0854|5end_hypothetical_protein_841335..841565_POSITIVE 333 99 54 53 13 NC_009009:SSA_0502|5end_Peptide_ABC_transporter,_permease_protein,_putative_501554..501784_POSITIVE 333 65 22 212 167 NC_009009:SSA_0161|5end_hypothetical_protein_159445..159675_POSITIVE 326 100 52 222 175 NC_009009:SSA_0150|5end_hypothetical_protein_143936..144166_POSITIVE 316 79 31 174 117 NC_009009:SSA_0812|5end_hypothetical_protein_793443..793673_POSITIVE 315 115 74 223 182 NC_009009:SSA_2243|5end_Conserved_uncharacterized_protein_2239341..2239571_NEGATIVE 309 100 54 180 131 NC_009009:SSA_0452|5end_Nitrogen_utilization_substance_protein_B,_putative_451534..451764_POSITIVE 298 88 41 147 99 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 294 85 41 145 107 NC_009009:SSA_0978|5end_hypothetical_protein_983736..983966_POSITIVE 293 100 52 163 114 NC_009009:SSA_1821|5end_Acetyltransferase_(N-acetylase_of_ribosomal_proteins),_putative_1810610..1810840_NEGATIVE 293 100 56 156 114 NC_009009:SSA_1459|5end_RNA_methyltransferase,_putative_1467481..1467711_NEGATIVE 293 106 61 218 180 NC_009009:SSA_0469|5end_Precorrin-6B_methylase_2,putative_472310..472540_POSITIVE 292 114 73 219 180 NC_009009:SSA_0805|5end_Collagen-binding_surface_protein,_putative_787476..787706_POSITIVE 292 100 53 204 160 NC_009009:SSA_0335|5end_Phosphomevalonate_kinase,_putative_328792..329022_POSITIVE 290 65 30 150 110 NC_009009:SSA_0725|5end_hypothetical_protein_710247..710477_POSITIVE 287 99 54 187 129 NC_009009:SSA_1341|5end_Carbamoyl-phosphate_synthase_large_chain,_putative_1359827..1360057_NEGATIVE 287 111 72 160 122 NC_009009:SSA_0692|5end_D-Ala-D-Ala_adding_enzyme,_putative_676370..676600_POSITIVE 283 100 54 64 16 NC_009009:SSA_1466|5end_Prephenate_dehydrogenase,_putative_1473111..1473341_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 399 102 61 84 42 NC_009009:SSA_0679|3end_DNA_repair_and_genetic_recombination,_putative_662452..662602_POSITIVE 359 100 51 73 30 NC_009009:SSA_0467|3end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_471795..471945_POSITIVE 356 120 72 105 62 NC_009009:SSA_0267|3end_ROK_family_protein,_putative_260873..261023_NEGATIVE 326 120 76 99 68 NC_009009:SSA_2301|3end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2302669..2302819_NEGATIVE 315 115 74 87 46 NC_009009:SSA_2244|3end_Arsenate_reductase,_putative_2239477..2239627_NEGATIVE 315 67 21 112 60 NC_009009:SSA_0686|3end_Fe2+/Zn2+_uptake_regulation_protein,_putative_670079..670229_POSITIVE 311 116 73 99 57 NC_009009:SSA_0452|3end_Nitrogen_utilization_substance_protein_B,_putative_452060..452210_POSITIVE 307 87 41 71 28 NC_009009:SSA_0921|3end_Zn-dependeant_threonine_dehydrogenase,_putative_932164..932314_POSITIVE 304 109 74 86 49 NC_009009:SSA_0304|3end_Bacterial_cell_wall_degradation_(CHAP/LysM_domains),_putative_301888..302038_POSITIVE 304 120 74 115 70 NC_009009:SSA_0281|3end_hypothetical_protein_273963..274113_POSITIVE 297 99 58 71 18 NC_009009:SSA_2265|3end_Maltodextrin_phosphorylase,_putative_2261936..2262086_NEGATIVE 297 107 75 41 6 NC_009009:SSA_1544|3end_Conserved_uncharacterized_protein_1548314..1548464_NEGATIVE 297 101 61 40 5 NC_009009:SSA_0149|3end_hypothetical_protein_143833..143983_POSITIVE 294 85 41 148 110 NC_009009:SSA_0977|3end_3-isopropylmalate_dehydrogenase,_putative_983819..983969_POSITIVE 294 117 71 99 53 NC_009009:SSA_0876|3end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_protein,_putative_870861..871011_POSITIVE 293 100 56 71 29 NC_009009:SSA_1460|3end_Transcriptional_attenuator_LytR,_putative_1467566..1467716_NEGATIVE 293 71 37 132 93 NC_009009:SSA_0263|3end_Zinc_metalloproteinase_in_scaA_5'region,_putative_258246..258396_POSITIVE 292 111 74 51 13 NC_009009:SSA_1409|3end_DTDP-glucose-4,6-dehydratase,_putative_1421209..1421359_NEGATIVE 292 114 73 90 51 NC_009009:SSA_0804|3end_Phosphoglucomutase/phosphomannomutase_family_protein,_putative_787427..787577_POSITIVE 290 65 30 135 95 NC_009009:SSA_0724|3end_ABC-type_multidrug/protein/lipid_transport_system_(pediocin_PA-1_exporter),_ATPase_and_permease_components,_putative_710312..710462_POSITIVE